Rhys having an... admirer in Katagawa makes sense when you look at his list of accomplishments: he started out as a low-ranking "code monkey", was able to survive Pandora, singlehandedly brought down Helios (and likely took a chunk out Hyperion in the process), took part in a battle against a Vault monster and won, looted said Vault (alongside Fiona) and rebuilt the defunct Atlas corporation in only a few years. It's little wonder why he'd be a source of admiration (and possibly fear/envy) among people in other corporations.
In addition, Katagawa's obsession with Rhys mirrors Rhys' own obsession with Handsome Jack, solidifying Rhys' position as Jack's Good Counterpart.
Rhys is a tad more skittish than he ever was in Tales from the Borderlands. He's not exactly known as being the fighting type or bravest person in the universe, add that with him being on the losing side of an all-out corporate war with one really creepy stalker that's willing to kill an entire planet's population to forcibly acquire him and Atlas (with all the subtext that implies), and you can more or less understand why he's a nervous wreck in 90% of the times he speaks to you.
Early on, you give a damaged Vault map to Tannis, who retreats into her little shack to attempt to fix it (the entrance is a black wall that keeps the player out), taking barely a few minutes to repair (somewhat, it's still damaged but it works enough to display a single planet) what is essentially an alien artifact in a tiny shack in the middle of nowhere, that Tannis herself admits most of the Eridian race's tech has stumped the brightest human minds with the corporations funding their research. With the reveal that Tannis is a Siren with the ability to Phaseshift (manipulate "anything with a current", i.e. electronics and machinery, possibly including the map), it might be possible that is what she used to repair it, as opposed to whatever research equipment she has in that tiny shack.
Who was the last Siren with that kind of power in the series? Angel. Fittingly, during Angel's tenure, Tannis, for all intents and purposes, was just a regular human, and it's only until Pain and Terror infuse her with Eridium that her powers finally begin to show. Coincidentally, back in 2, Jack kept using Angel's powers by infusing her with Eridium.
In Promethea, a side mission has you get some blood from a donor. Instead of using any sort of caution, or just hitting interact and having the operation done normally, you instead have to hit melee and cut/bash the donor's arm off. This could be a Call-Back to Borderlands 2, where Doctor Zed asks you to perform surgery by making a "small incision, just above the sternum", where you handle the situation in the same manner, to which he responds "close enough". Apparently, Vault Hunters don't make good doctors.
The monks of Athenas having a vow of peace and non-violence, as well as the history of the world having Siren rulers, goes a long way to explain why a single Siren like Maya was expected to dominate the entire planet through fear. It also explains why Maya was able to just kill the leader of the Impending Storm and walk away, and reassume command once she returned.
You may have noticed that the Nomad bandits from Borderlands 2 have disappeared, while most other bandit sub-types are still around. However, if you listen closely, you can still find them... but they're now working for Maliwan as their Heavies. Considering the general psychopathy among the Maliwan soldiers you encounter, it's likely that many of their troops were recruited from bandits and criminals who were slightly more stable than the ones who joined the Children of the Vault.
In Greek mythology (references to which are everywhere in Borderlands as is), Typhon is a dragon with a hundred heads that Gaia, or Mother Earth, sent to defeat Zeus after he took out his father Cronus. Typhon and his mate Echidna had many monstrous children. What's this got to do with Typhon DeLeon, you may ask? Well, when you meet him later, he mentions that he has two kids, and that they grew up to be guess what? Monsters.
Also in Greek myth, Calypso was a nymph who kept Odysseus on her island for seven years. Her name comes from the Greek word meaning "to conceal/deceive." It's no coincidence, then, that the Calypso Twins did their fair share of deception in order to amass such a large following.
The names for the tattooed women, "Sirens", seems a tad non-indicative, as their powers never rely on voice and seldom hypnotize people (Maya's "Thoughtlock" ability is the only example). However, Tyreen makes it meaningful in a different sort of way. She and her brother manage to charm the bandits across the galaxy and frequently make use of propaganda centers and radio stations to spread their influence, all the while luring many of their followers to their death for sustenance.
Also, when you look at the Sirens we know, each of them DOES somewhat hypnotize others through their voice and presence. Maya was instrumental in the leadership of the Monks, first as a mere figurehead and "voice" for them, and later as a true leader. Lilith leads the Crimson Raiders along with keeping them together, and has (inadvertently) created at least a couple cults that worship her. Angel both led and misled the Vault Hunters as an enigmatic voice over the ECHONet. The only one that we haven't seen deliberately influencing and directing people is Amara, and that's because she's far more focused on fighting anything she runs into than her predecessors... and even then, she's a celebrity crime fighter back on her homeworld, to the point of needing her own publicist and manager to maintain her personal media presence.
Commandant Steele from the first game led an elite group of Atlas soldiers to The Destroyer's vault, and Angel from the first two games manipulated two groups of vault hunters to do Jack's bidding (and would later repent for it), regarding the non-playable Sirens from the previous games for this entry.
In much the same way that the second group of Vault Hunters seemed to outclass the first, the current crop seem much more capable and experienced, both in character and mechanically. This would explain, for instance, the greater degree of customisability of action skills and augments, whereas previous generations of Vault Hunters only had one.
Lilith's Siren abilities were largely self-taught in a vagabond lifestyle, and she wasn't concerned with finding out anything more about her heritage. While Maya received some instruction and training, she got it from a group of monks who wanted their own pet superhuman and so probably didn't tell her everything she could do, along with discouraging her to think for herself. On the other hand, Amara has been making constant use of her Siren power for years as a vigilante against her world's criminals. Self-taught or otherwise, Amara's fought for far longer and without being manipulated by someone else into not exploring her potential, so she trumps both previous Sirens in sheer experience, explaining her versatility (her three base abilities) and being able to alter the ways they work (the augments and elemental modifiers).
Axton was a professional soldier, sure, but a bit of a maverick and loose cannon by the sounds of some of his ECHO logs, and he deserted while taking a customizable Dahl turret. Roland similarly deserted the Crimson Lance, but out of moral dissolution with the Crimson Lance. Moze, on the other hand, was part of an elite squadron of mechanised infantry with a fearsome reputation and retains her soldier's discipline (mostly) all of the time, and she left her post with an advanced Vladof mech at her command. In every sense of the word, Moze's got her predecessors outgunned. Alternatively, while Salvador is a civilian fighter who focuses on brute strength through More Dakka and whose ammo regeneration relies on his action skill, Moze is a trained soldier whose ammo regeneration can be triggered through multiple means.
"Jack" AKA Timothy Lawrence was just some poor schmuck randomly chosen by the real Jack to be his body double. While he proved to be a very capable fighter to his own surprise, he was thrown in at the deep end and cannot even remotely compare to Zane (who he is most similar to), a seasoned veteran and (retired) professional hitman with a very long career behind him, to the point where Zane treats the events of BL3 as an enjoyable vacation instead of a dangerous galaxy-spanning war. Alternatively, while Wilhelm is a mercenary with no qualms with who he works with and his drones mainly focusing on health and shield regeneration, Zane has moral standards and concentrates firepower in his single drone or protection with his force field.
FL4K is the hardest to pin down: they are likely self-taught as Mordecai was, the only difference being their robot brain could help them learn a lot faster, plus their background as an archivist bot could give them access to all the information they need on the creatures they tame. This is shown by FL4K taming three different attack animals, and how they're able to cultivate those animals into Badass variants. Word of God also states they are several hundred years old, giving them more time to learn. On a lesser note, both FL4K and Claptrap are robots who naturally resist fire attacks but take more damage from corrosive attacks, with FL4K obviously being the more competent vault hunter.
Why do the Children of the Vault rename themselves the Children of the Firehawk and (maybe) stop being so viciously psychotic? For the duration of the game they'd been worshiping Tyreen who called herself a god and would kill her believers at the drop of a hat and for no reason. Lilith, on the other hand, managed to stop the apocalypse the Twin Gods had started, plus branded Elpis with her logo, marking her as more powerful than Tyreen and Troy in addition to saving the COV members. She's stronger and benevolent - much closer to a god worth the worship.
For gameplay purposes, however, the COV are still fought in the post-game. Their radio broadcasts proclaim that they will continue to fight in Tyreen's name no matter how badly they're beaten down. That, and given how much trouble even God Queen Tyreen had getting them to ally with Maliwan (an ECHO log shows her trying and failing to hammer this into her cultists' heads), it isn't much of a stretch to assume any transition from enemy to ally would take quite a while.
Maliwan's presence on Nekrotafeyo would explain a lot of things - mainly, the new, almost alien like design of their guns, as well as the ability to shift between two elements. Rhys claimed that the research benefits of studying a mere Vault Key fragment would have kept Atlas afloat for potential decades. Now imagine what Maliwan could do (and probably did) with free access to a whole planet full of potentially still-functioning Eridian technology.
Early on in the game, when the Vault Hunters arrive on Promethea, it's revealed that the Calypsos are already there, and have been, as Tyreen said, "for ages". It's the same story with Eden-6. And whilst on Promethea, you get a call from Tyreen wherein she indicates she was about to drain an entire newly-pledged bandit clan of their energy, seemingly for shits and giggles. But that's exactly it - she wasn't draining huge swathes of her followers just to satisfy her hunger. She was using them as fuel, probably along with some Eridium, to teleport entire armies from planet to planet with Lilith's powers!
Also, on Eden-6, most of the bandits come from the population of the prison. An ECHO recording from Clay indicates that the prison gangs had already sworn allegiance to the Children of the Vault long before the Calypsos arrived and left Wainwright as the heir. The rest of the bandits were teleported in later by Tyreen.
The absence of the Borderlands/Pre-Sequel Vault Hunters from previous titles - those who are still alive or not working for the Calypsos like Aurelia anyways - may be a bit odd, given that a threat this big should warrant them all being pulled in, but besides the fact that this is a new Borderlands installment and thus new heroes are required, it's been seven years, long enough for everyone to have moved on from the Crimson Raiders. After all, Jack and Hector are dead, their respective armies crushed and scattered to the four winds, so naturally, it'd make sense for the Borderlands 2/Pre-Sequel Vault Hunters to put down their guns and go do something else for a change, which conveniently leaves (most) of them far from the events revolving around the Calypsos. And going by the games and their respective personalities...
Axton, being a model, is likely somewhere far from the frontier worlds the story takes place on, and his absence from a developed world like Promethea can be explained in that he never met Rhys, and while he might still be in contact with Zer0, his occupation as a model means he's either done with or disinterested in the concept of jumping into another firefight to save a planet that routinely attempted to murder him on a daily basis. His most recent gig is being the co-host of the Arms Race.
Gaige is an outlaw who specifically went to Pandora to get away from the law, and an Echo log found in-game indicates the Holloways are still chasing her. She may have accordingly chosen to have left to protect the Crimson Raiders from getting involved with the feud she has with the Holloways, which she may see as a personal thing that she needs to handle by herself, as opposed to dragging the Raiders into it and escalating the feud into some kind of a war. She returns in the Love, Guns, and Tentacles DLC, and now works as a wedding planner.
Seeing as he's a bit of a family man, Salvador may be off visiting his beloved Abuela, and given that he's not exactly the most responsible of the Vault Hunters, if he was given a method of contact, he likely lost it. That, or his penchant for chaos means he's simply gone off to go trash things somewhere else. Like Axton, he's now the co-host of the Arms Race, probably to pay off debts from The Lodge at Xylourgos.
Athena is likely off somewhere attempting to live a peaceful life with Janey, and would likely have no interest returning to her former life as an assassin/mercenary, especially after the events of the Pre-Sequel and how Lilith treated her then.
Timothy, having gone into the movie business, is probably busy filming whatever movie he's busy filming, and thus unavailable due to his shooting schedule. At some point during his career, he got trapped in the Handsome Jackpot casino, and he remains there until this game's Vault Hunters free him.
Krieg's primary motivation for joining the Crimson Raiders and their fight lay in wanting to exact revenge upon Handsome Jack, and because he liked Maya. Given that Jack is dead and Maya has moved on from the Raiders, he has no reason to stay with them. That, and he's a psycho, the kind of person the Raiders shoot on a daily basis. Assuming he didn't leave of his own volition, without the other Vault Hunters with him to keep his homicidal urges pointed in the right direction, he would've probably become very unwelcome sooner or later. Even if the Psycho half felt that was the case, he has worked with the Crimson Raiders on a few missions against the Co V and was even offered to join their afterparties.
Of all the bandit types why haven't the Rats been recruited into the COV? Apparently the Calypso Twins found them too creepy to work with. That and they're skin and bones, not much for Tyreen to feed off of.
The logic of the weapon manufacturers and what they make and the changes made between the last game and this one:
Atlas: With Rhys in charge, their handguns and rocket launchers are now wrist-mounted. Their assault rifles still require two hands to use though. All 3 weapons come with alt-fire trackers that lock-on to the enemies. Submachine guns wouldn't benefit much from homing trackers and bullets, nor would shotguns or sniper rifles, hence their absence in Atlas manufacturing. However with 3 exceptions most of their guns don't have any elemental enhancements at all as the grenade mods fill that niche. This is due to Maliwan and the COV invading Promethea, which no doubt interrupted any attempts to enhance their firearms with elemental powers, given that there's a planet-wide invasion going on.
COV: They still don't make sniper rifles, for the same reason as their bandit predecessors; their troops have neither the discipline, patience or tactical acumen to wield them effectively. COV guns drawing ammo from the backpack effectively eliminates manual reloading, allowing their troops to fire non-stop...which is basically their one and only strategy in combat. However, this comes at the cost of overheating and repair if the guns ever break, hence the need for spare parts and water bottles, squirt guns and portable hoses. Also they had to abandon their shotguns and SMGs, probably because they didn't mesh well with the More Dakka philosophy being bumped Up to Eleven. You can imagine the bandits not being happy about this, as it hinders them to some extent in close range, which, admittedly, is somewhat made up for them retaining their trademark Action Bomb and Close Quarter Combatant tendencies. Also the Calypsos tried to compensate for this loss by having their cult join forces with Maliwan which has both shotguns and SMGs followed by allying with Aurelia Hammerlock (with Troy literally getting into bed with her) to acquire the vaunted Jakobs shotguns.
Dahl: They still make pistols, SMGs, sniper rifles and assault rifles - pretty straightforward military gear, but precise military gear. Dahl prizes accuracy and minimal collateral damage. However after receiving complaints about their guns being restricted to aim at the sights to bring out their full potential, and after no-doubt witnessing first-hand (via the events of 2 and the Pre-Sequel) what happens if people armed with their weapons get caught at ranges where the fire-mode is ineffective, the company decided to install alt-fire modes to their weapons. Now Vault Hunters can burst fire or go full automatic at both the hips and sights! Now if only they can break away from their Dirty Coward / Paper Tiger tendencies.
Hyperion: After having their asses handed to them by the Vault Hunters and Handsome Jack's demise by said Vault Hunters, Hyperion decided to make some changes to distance themselves from their tenure under Jack. First off getting rid of handguns due to their awkwardness, lack of real killing power despite their accuracy, and just being associated with Jack as the weapon that murdered a renowned Vault Hunter. Second, adding shields while aiming to their shotguns, SMGs, and sniper rifles no doubt helps their intended audience - the corporate layman, of whom is likely neither heavily armored nor particularly battleworn - survive in Borderlands' cutthroat corporate world. Finally shoving the Jack A.I. into an SMG and installing Tediore firmware diversified the company's portfolio, going from being the guns that were the most accurate to guns that are more adjusted for the dynamic battlefield.
Jakobs: No rocket launchers or SMGs, entirely for aesthetic reasons. Their old school of thought - extremely high damage, critical modifiers and a strong emphasis on sheer damage over everything - remains unchanged. However some of their purple quality or higher assault rifles are now hand-cranked - referencing the early Gatling Guns - and any critical hit made by their weapons will have the bullet ricochet to the next target, allowing a skilled marksman to make the most of their shots. Their shotguns also have the potential to possess larger magazines, likely due to Wainwright's preference for them given his disability.
Despite their reputation from having low-tech yet effective weapons, some of the Jakobs guns have alien barrels. Why? Possibly due to Clay modifying them for aftermarket (remember that he created the Rogue Sight revolver) to help out his adoptive brother Wainwright and avenge his father-figure Montgomery Jakobs who was slain at the hands of Aurelia Hammerlock and the Calypsos. Clay probably also created the Hellwalker to counter Aurelia's ice powers.
As a matter-of-fact Wainwright dreaded the notion of his family's weaponry in the filthy hands of the COV. It happened once before when one of his family's manufactured shotguns fell into the hands of an extremely uncouth brute named Sledge who claimed it as his own. Then it happened again right after murdering Wainwright's father, The Calypsos stole another legendary shotgun, desecrated it with their graffiti and teleported back to Pandora and gave it to Hot Karl whom rebranded it as "Sledge's Shotgun".
Maliwan: No assault rifles, as per tradition, but they have dropped the rocket launchers for shotguns, likely to fit in with their "stylish corporate executive" aesthetic. Maliwan build weapons to make their designers feel clever, after all, which means either weapons that are precise (pistols, sniper rifles) or weapons that let them push the boundaries, with their tech submachine guns as a speed test. With Katagawa in charge of Maliwan, the rocket launchers were dropped in favor of shotguns as he felt that shotguns give the enemy a personal sense of fear. That and he was probably tired of hearing complaints from Torgue.
They also added in alt-fire elemental capacitors like incendiary/shock to deal with enemies that have shields or incendiary/corrosive to those who have armor, likely as a result of finding out the hard way that having a powerful elemental weapon means absolutely nothing if the opponent in question can No-Sell the oncoming fire.
Tediore: After having their asses handed to them by Vladof's Iron Bear Corps, Tediore decided to make changes to their reload system. Instead of being simply grenades, they become turrets that fire down on the enemy or drones that hunt down their prey. However they had to abandon their rocket launchers for this feature to work and other companies still see Tediore as a joke though they won't be laughing as much when hordes of Baby Maker, Turbo Ten Gallon, Fire Musket, Scorpio, Mother Too, Smart Gun XXL, and Dark Army drones move in for the kill.
Plus, the newfound diversity of Tediore means that they have something other than being a very cheap brand to buy from and their dubious honor as useful Vendor Trash going for them. Their guns having a wide range of gimmicks and abilities means that people who would've either passed them over or sold their weapons to the nearest vendor the moment they had the opportunity will now be taking them seriously when picking out weapons to carry into battle.
Torgue: No submachine guns or sniper rifles still apply here. When Torgue was reinstated as the company face he was forced to compromise by having weapons get elemental enhancements since explosive damage is no longer considered an element and the new radiation element could fill the niche of making things explode. On the other hand having sticky gyrojets alt-fire on your rifles, shotguns and handguns is perfect due to enemies having a nasty habit of escaping your line of fire, and the gyrojets mean that there's not much they can do once an explosive bullet is latched onto them. Torque saw how terrible the E-Tech pistols were and decided to make sticky bullets with more damage. Apparently Jakobs liked the idea as well when they created The Duc pistol based on Torgue firmware. So did Hyperion and Dahl with their Proprietary License and Kaoson SMGs respectively.
Vladof: No shotguns or submachine guns also still apply here. However after the Darzaran Bay Massacre (which unbeknownst to the company Moze was the sole survivor), Vladof decided to make changes by adding more firepower to their weapons so incidents like that never happen again. For their alt-fire modes, we have zip rockets, tasers, grenade launchers, rocket launchers, mortars, double-barrels, and shotguns. As a matter of fact, Vladof created the Sickle, an assault rifle with shotgun properties as an homage to their discontinued Hammer shotgun from the first game.
All of this also makes sense when one takes into account that Vladof - like every other company - has learned from the weaknesses of Crippling Overspecialization that were demonstrated in the first three games. More Dakka, while effective, will only carry the company so far, so their subsequent foray into all sorts of under-barrel attachments is at least rooted in making their weapons more competitive with the other companies.
Cryo and Radiation deal decent damage to both armor and shields respectively though not as much as corrosive and shock. Why? Prolonged exposure to extreme cold can make even the toughest of armor brittle and radiation can interfere with electronics which shields are made out of.
On a similar note, beside the fact that the other elements are more effective, Slag's absence from the game is quite simple. Jack's Hyperion had a monopoly on Slag weapons due to their extensive work with Eridium. With Jack dead, his incarnation of Hyperion burned to the ground, and Pandora no-doubt having a reputation as being a graveyard for any corporation that dares set foot on it, Slag in a weaponized form simply doesn't exist anymore, since no one's around to research Eridium and weaponize the byproducts.
Atlas and Jakobs are among the few weapon manufacturers who side with the Crimson Raiders. Coincidentally, both of these companies tend to ignore elemental attacks, save for a few unique examples. Meanwhile, the villain company of the week is Maliwan, who specializes in only elemental weapons.
Additionally, the CEOs that work for those respective corporations have good reason to ally with the Vault Hunters. Besides the fact that the Crimson Raiders singlehandedly-ish save him and his company from utter destruction, Rhys has history (most of it positive) with the Pandoran Vault Hunters, almost all of whom were affiliated with the Crimson Raiders. Similarly, Wainwright is romantically involved with Alistair, a longtime friend of the Crimson Raiders. Even without witnessing the heroic actions of the Crimson Raiders first-hand, both CEOs have spent plenty of time with people who were affiliated with them in some way, and therefore should have a good idea of the Crimson Raiders' mandate.
Kill-a-volt is likely using the Transformer shield himself, seen by him being completely immune to electric attacks, hence his higher drop rate of said shield.
Alistair Hammerlock seems like a perfect match for Wainwright Jakobs, being a hunter with a preference for sniper rifles and precision shooting, which no doubt compensates for Wainwright's crippled eyesight and dependence on shotguns. It helps that Alistair also made use of Jakobs weapons before meeting Wainwright, as shown in the Big Game Hunt pack in the previous game.
Aurelia Hammerlock being a villain under the employ of the Calypso Twins makes sense when you remember that she was part of the villainous half of the Pre-Sequel's Vault Hunters, but unlike Nisha and Wilhelm, she lacked any loyalty to Handsome Jack and Hyperion, sparing her from death for a while when Hyperion made enemies. Only the chance to spite her brother gave her the push to become a target of the Crimson Raiders.
Aurelia's boss fight shows two signs of frigid brilliance (pun intended): 1) she very clearly states she doesn't give a damn about the "poor" (basically everyone in the whole universe), so the CoV enemies are affected by her attacks as much as you are, and 2) she's killing the cannon fodder bandits, enemies you use to get Second Winds; she lets them live just enough to surround you and inflict damage, aims all of her attacks at you, and then tries to off them before you have a chance to recover from Fight For Your Life. It helps to remember she was a Vault Hunter, so she knows about that.
Why E-Tech weapons don't appear this game? Apparently the weaknesses of said weapons far outweighed their strengths in-universe. E-Tech Snipers were impractical due to being unable to score critical hits, assault rifles being real ammo hogs and unable to deal real damage at all (Bandit Blasster rifles were the worst in addition with the mediocre reload time and it REALLY sucked if you were equipped with a non-elemental), the splatguns would have been decent were they not affected by gravity (two E-Tech shotguns made by Torgue were the exceptions) and Spiker and Dart pistols were just flat-out weak and unimpressive. Not even the vaunted Plasma Caster SMGs and Rocket Launchers (PRAZMA CANON, PBFG, Launcher, and Topneaa, which included the now-discontinued Norfleet from Maliwan) could compensate for the glaring flaws. Thus E-Tech was completely discontinued in favor of the more powerful alien tech barrels.
Hyperion's New-U stations working for the Vault Hunters seems like a Pet the Dog from the previously villainous company, but it could also be pragmatic assuming Jack's hatred for bandits remained.
3 of the 4 new Vault Hunter only have an inkling of who Handsome Jack was. Zane is a different story. Being an operative, he would know the in-and-outs of just about every manufacturing company across the Six Galaxies, especially Hyperion. He also probably knew his older brother Captain was gullible enough to fall for Jack's scam.
The Mayor of Trashlantis giving you only cosmetic items for completing his share of optional map-specific searches, as opposed to Torgue's and Ember's equivalents, makes perfect sense when you remember his stance against corporate greed and valuing material possessions, and the fact that he is a tailor.
Gaige's wholesome support of the marriage between Hammerlock and Jakobs makes sense when you remember that Jakobs weapons, with their modest magazines and potentially fast firing rates, were ideal for building Gaige's Anarchy boosts.
In the research logs, Eleanor and Victor never use the word "Eridian," only referring to "precursors," even though the ruins are clearly Eridian and Gaige conclusively identifies them as such. However, Eleanor and Victor are a lot older than they look; Gaige notes that all their tech is so old she's barely even heard of it, and she's a bit of an old tech nut. It seems like they were some of the first people who found Eridian technology, before that word had even been invented.
Moze's Iron Bear progression in general. Moze outright states that the parts for Iron Bear that she needs for repairs and enhancements are not cheap, so her progression as a Vault Hunter can be seeing as her getting paid and being able to upgrade/fine tune her mech unit. Also while Iron Bear is a force to be reckoned with from the start, it canonically did have a rough time in Darzaran Bay and thus it's not in its best condition at the start of the game. It likely had all or most of the upgrades that Moze can get in this game, but she's now flying solo and can't requisition those from Vladof directly any more.
In hindsight, there's a lot of hints as to the true identity of the Company that once ruled and eventually nuked Gehenna. The focus on Core crystals, esoteric technology, bioweaponry, and general atmosphere makes the Company seem like a long-dead former player in the Borderlands universe. It's not - it's the Jakobs Corporation. After all, their guns are everywhere, their chests are everywhere, and it's a western - the era with which Jakobs is most associated. It's not even the first time we saw an aesthetic combining elements of the Wild West and Japan - the Jakobs manor blends elements of both Eastern and Western architecture. Most damningly, when the swindler General Stickly tries to sell you "original Company stock," it's a Jakobs shotgun.
Borderlands 3 goes a long way toward explaining some odd elements from The Pre-Sequel.
Lilith mentioning that the Guardians didn't try to stop her makes a lot more sense after decoding the Eridian archives and learning that a Siren helped the Eridians craft the Great Vault and that Elpis is the Vault Key for it. They likely viewed her as a potential ally by default, and knew that she was trying to stop the smaller Vault on Elpis from being misused.
The Destroyer's eye being powerful enough to destroy Elpis makes a lot more sense with the revelation that the part that we fought and destroyed was just a tiny sliver of the real creature, which was able to easily consume stars.
Zarpedon trying to destroy the entire moon instead of just targeting the Vault makes a lot more sense, because the entire moon is the Vault Key, with the Vault just being a small part of it.
Dr. Benedict differs from most Borderlands villains by being a Knight of Cerebus with nothing funny about him. This makes perfect sense, as the version we see is just a bad memory — the manifestation of Krieg's hate/fear of the guy, which has been festering in his mind ever since he became a Psycho. While he clearly wasn't a very nice guy in life, there's absolutely no way Krieg would, could or should haveany positive memories of the monster who destroyed his life.
The new action skills.
Fl4K didn't simply acquire a Loader Bot as a pet out of a whim. They remembered Joy, the friendly Loader Bot from the Handsome Jackpot side mission Heart of Gold, who died from a defective power core. They also saw Gaige break down in tears after witnessing Deathtrap "dying". Fearing a similar fate, Fl4K adopted a Loader Bot in the hopes of sharing and passing down their centuries-worth of knowledge before their own eventual end arrives.
Amara developed the Phaseflare skill to honor the memory of Maya, who had a similar Melee Override Skill called Scorn, which fired a large orb of Slag at her enemies.
By coincidence Atlas created the Res handgun, which fires healing bullets, to honor Maya as well as she had that skill to heal/revive her fellow Vault Hunters.
Moze began to realize that Iron Bear, while powerful, was severely limited by its size; it's a fairly common occurrence in-game for Iron Bear to get trapped in a room since the door's too small, wasting its firepower or causing it to be destroyed. She sought out the help of Tannis, Ellie and Gaige to create a modulator that summons Iron Bear in a more compressed size, thus was born Iron Cub. The damage may have been reduced but it remains a credible threat now that it can gain access to areas that restricted its larger counterpart.
Some time after the Handsome Jackpot heist, Zane acquired some schematics based on Wilhelm's Vengeance Cannon and developed the MNTIS shoulder cannon. While not powerful as the Vengeance Cannon, the MNTIS is more versatile as it can be used more than once, can freeze or shock enemies, drag them closer to inflict more damage, and doesn't require Zane to be at low health to summon it.
Tyreen's power to steal strength from others and give it to her brother is a corrupted version of Maya's Harmony skill tree, particularly Sweet Release and Life Tap. Let's all be glad Maya's a really nice person, or else there'd be two of them.
Just outside the Holy Broadcast Center, you can find a derelict bus with graffiti on it. The graffiti depicts 6 silhouettes labeled "Vault Hunters", and four of them are crossed out. Taking into consideration that only two of Borderlands 2's Vault Hunters make a physical appearance, the implications are disturbing.
This is one is slightly lessened by the fact that this graffiti is a Recycled Asset from The Pre-Sequel!! (See the bandit truck from the opening cutscene.) Adding to this, Borderlands 2 establishes that the Vault Hunters we see are not the only ones out there (Handsome Jack is said to have killed many before the start of the game.) So while our Vault Hunters may be okay, this just means that many others didn't make it.
With the exceptions of Salvador, who is unaccounted for, and Maya, who is dead as per the storyline of 3, the Borderlands 2 Vault Hunting team is strongly suggested or outright confirmed to still be alive, given that Axton has apparently retired from frontline service as a Vault Hunter and taken up a day job as a model, Gaige is still being hunted down by the Holloways while working a regular job as a wedding planner, Krieg is apparently still wandering Pandora and is now sane enough to hold a coherent conversation, Zer0 is working for Rhys as his personal bodyguard and Salvador is apparently traveling around the galaxy.
One of Typhon's logs points out that a lot of ships crashed on Eden-6 like something was attracting them. When you fight the Graveward, note how one of its arms has rocket boosters and you may have a reason why.
Ava's actions in the first vault leads to a chain of events that nearly let the Destroyer free. Had she not been in the vault, Maya wouldn't have grabbed Troy. If Troy hadn't been grabbed, Maya would never be leeched, and the twins wouldn't be able to Phaselock Elpis and try to set the Destroyer free.
However, it was Typhon DeLeon's Deconstruction of Overprotective Dad that made the Calypso Twins into who they are which led to the events of the game. Typhon may have been the first Vault Hunter but he was still human.
The people of Elpis, including the citizens on civilized settlements like Concordia, were likely obliterated in a cataclysmic event when the Calypsos phaselocked the entire moon and dragged it close to Pandora. Even if there were survivors, then Lilith blasting herself onto the surface and searing a fiery phoenix would have immolated half the moon's population.
The whole deal with the now adult Tina being really promiscuous is kind of disturbing when you considering promiscuity is often a side effect of having an abusive childhood, and we all know Tina had a really bad childhood, starting from having her parents killed right in front of her.
The fact that Wainwright Jakobs learning that the monsters that killed his father in cold blood were the children of Typhon DeLeon, the man who gave him advice on using shotguns and created the Jakobs' trademark slogan as well as being a friend to Montgomery Jakobs would have been disheartening as well as having Typhon's good name being dragged through the mud posthumously for siring two megalomaniacal hellions with God complexes. For this reason Winnie would've kept this secret from most of the general public.
Just exactly how long have The Bonded been victimizing people? It's suggested further up on the page that Eleanor and Vincent are extremely old. Wainwright and Gaige both describe the tech of Xylourgos as being extremely old (In particular, Gaige recounts that her grandfather had the Delta-3 tape you find) and they seem to predate the discovery of the word "Eridian," which could place this figure at anywhere from over seventy to several hundred years. And more importantly, can we actually be sure that any of the Vault Monsters slain are actually dead?
The fact the Psychos can be created as well as being exposed to alien technology puts a chill in your spine. How do we even know which is which but vault hunters will be too busy fighting for their lives for those answers.