It seems like a plothole that Taichi and Yamato can suddenly digivolve their Digimon into Ultimate, Megas, and then Fusion/DNA/Whatever digivolve into Omni/Omegamon. But at the end of 02 a new barrier was created by BlackWarGreymon and Oikawa, meaning that the crests would no longer be needed to power it. This wouldn't be the first time the Digidestined have used the power of the crests without the physical crests themselves, and the digimon did fully expect to regain the ability to evolve back in the old series.
It's actually quite important to know that Mimi's still been living in the United States right up to the beginning of Reunion. First, it emphasizes that the Digital World has been closed off worldwide, and thus all the Chosens around the world have been separated from their Digimon, as Mimi and Palmon had been separated as well. Second, as disturbances and breaches from the Digital World tend to originate in Japan and then spread worldwide, it would leave the rest of the world unassuming of the disturbances in Japan at the beginning of Reunion; Mimi herself wasn't even aware of the Digimon reappearing until she landed in Tokyo.
One involving the Greek Alphabet: Alphamon is the first Mega to appear in the movie, and is the first Digimon seen in the first five minutes of the movie, while Omegamon is the last Digivolution and Digimon shown in the movie, while also being the second and last Mega Digimon shown.
It might seem like the team were a bit fast in welcoming Meiko and Meicoomon onto the team, but the Chosen Children have always been quick to add new members, welcoming the 02 kids and the International kids to the team almost as soon as they met them. Mimi's particular enthusiasm about Meiko joining the team also makes sense given that she's lived in America for a while now and has spent a lot of time with fellow Chosen Children there - she's more familiar than anyone else with Chosen Children outside of their small group.
Savvy fans of the series might find Alphamon Ouryuken being matched evenly with Omegamon to be rather jarring. But remember, while Alphamon Ouryuken is stronger than Omegamon as a species, this particular Omegamon is probably much stronger than other incarnations of itself. After all, the Wargreymon/Metalgarurumon that formed it went through immense Level Grinding during the original series. (Best demonstrated by how they never really gained a new form against the Dark Masters, but went from being curbstomped to defeating them without too much trouble later on) As such, it wouldn't be a stretch to assume that Omegamon here had gained enough experience to be able to match the naturally more powerful Alphamon Ouryuken. Digimon with human partners are also implied to be stronger than their wild counterparts, so there is also that to add on to the table. Plus rather than being a natural Omegamon he's the fusion of War Greymon, Metal Garurumon and all the data from thousands upon thousands of emails. That's A LOT of potential crammed into one package.
It's also worth noting that Digimon power levels can vary wildly between incarnations (the X-Evolution Omegamon could be wrong footed by two X-Antibody Digimon while the Adventure Omegamon effortlessly wiped out thousands of Mega level Digimon).
The most sensible logic is this Alphamon is actually far weaker than normal. Alphamon is a user of the Alpha inForce and can manipulate time so his attacks unleash infinite damage with his green orbs. This series' Alphamon can't kill any of the champion leveled Digimon, so he's therefore much weaker and Adventure Omnimon can rival him.
Agumon and Garurumon cycling through their entire evolution line not only allows for some visual coolness but can also be taken as the "real world" appearance of warp Digivolving.
Even better; they each take turns attacking at each stage of evolution. They're working together to tag team their opponent, one digivolving whilst the other covers them, weakening their enemy as they both grow in power. Really shows how far they've come in developing their battle strategies over the course of the entire series and how in sync these two in particular are with each other.
Regarding of covering each other as they evolve through each level, one could be reminded of the battle against Infermon; because Keramon cheated by skipping a level to immediately go Ultimate, Greymon and Kabuterimon wasted effort and time to fight an opponent above their league and realized it too late. Their defeat is ultimately because Infermon sucker-punched them in the middle of evolution. Thus, their strategy of taking turn fighting and evolving is them learning that transformation is not a free action.
When Joe mentions that he has a girlfriend, everyone else is either shocked or in disbelief...except Izzy, who just asks "You have a girlfriend, Joe-sempai?" Now why would Izzy be the one who believes him? Presumably because with Joe taken, one potential obstacle to him being with Mimi is out of the picture.
Takeru and Hikari going to Ken's house to check for him may sound stupid at first since they just saw him as the Digimon Kaiser. However, the only logical reason that they did such a check is to rule out the possibility of evil clone, hologram or even an imposter. Considering the reveal at the end of Confession, they may be on to something.
Tailmon is the first to realize the full implications of 'rebooting'. She's the only Digimon who actually had a history and backstory before meeting her partner, said history and backstory making her relationship all the more special and important to her. So of course she'd be hit all the harder with the prospect of forgetting all that.
It also helps that she's an Adult leveled Digimon. Of course, an adult would realize the implications faster than a child.
A sort of dark Fridge Brilliance: When do things start going wrong for the good guys during the battle with Meicrackmon? When Angemon, whose crest is Hope, succumbs to the Virus. From that point, the digimon start turning on a dime until only Tentomon is left. When Angemon fell, they quite literally lost any hope of preventing the Reboot.
Throughout Tri, the DigiDestined have all acted against their Crest or have their Crest turned against them.
Tai, the Crest of Courage, is scared of fighting Digimon out of fear that he might cause damage.
Matt, the Crest of Friendship, is actively antagonizing one of his closest friends, Tai.
Sora, the Crest of Love, is conflicted loving Biyomon, but Biyomon having forgotten Sora, hates her for being overbearing
Izzy, the Crest of Knowledge, is letting his desires to know about the corruption overrule his ability to relax as he pushes more and more people away from him. Not only that, but other people have knowledge that is crucial to his research, but refuse to share it with him.
Mimi, the Crest of Sincerity, ends up being Brutal Honesty and it ends up making her seem pushy to the point of annoying.
Joe, the Crest of Reliability, ends up being unreliable in the first movie as he focuses on his studies and it isn't until Kari talks some sense into him that he ends up being a member to the team.
TK, the Crest of Hope, is hit with soul-crushing despair upon learning that Patamon is infected.
Kari, the Crest of Light, witnesses her brother falling with her wanting off a cliff and is broken with darkness.
As the Mysterious Man said "A tearful reunion." when he and Maki were looking at the reunion between the Digidestineds and their Digimons, Maki smiled, because she thought that is what is waiting for her when she reunites with Tapirmon, her own Digimon partner.
Not only that, since the reboot is the Digital World equivalent of a System Restore back to the moment before the Digidestineds and their Digimons met, she thinks Tapirmon will be safe from the memory wipe when it is brought back since it died long the before the events of Adventure.
One group insisting to another that they are their partners, with the latter initially veering away from stranger suspicion. Are we talking about the beginning of Adventure for the humans or the end of Confession for the rebooted digimon partners?
In the prologue to Loss you can see that Daigo and Maki are among the original Chosen Children, with a pair of goggles alongside Daigo: he fits the "Ta-/Da-" themed naming of Digimon's prior goggle guys!
Many people were put off by the fact that Metalseadramon and Machinedramon appeared as merely mindless monsters, instead of the powerful warlords they were before. But when you think about it, it makes sense. These guys were literally out to take over the Digital World and shape it to their desires. If Yggdrasill is going to use them as foot soldiers, it sure as hell isn't going to keep their evil minds intact.
In Loss, how are the partner digimon able to reach Mega level despite being inexperienced because of the reboot? The answer is the chosen children have always been the catalyst for evolution. To reach champion level the partner digimon and chosen children had to establish their bonds. To reach ultimate level, the chosen children had to tap into the power and represent their given crests. In Tri, reaching Mega level is knowing and overcoming the "darkness". Taichi, Yamato and most of the others have already gone through their stages of growth needed for digivolution, so once they reconnect with their partner digimon, Mega evolution becomes simple.
Despite not participating, Mimi assures Palmon she could have joined the other Mega level partner digimon as well because they have reconnected as well and achieved Mega form prior to the reboot.
In Loss, takes the combined efforts of Phoenixmon, Seraphimon, and Herculeskabuterimon to bring down Machinedramon, whereas Wargreymon was able to solo him in the original series. Why is he so much tougher? For starters, Wargreymon had both a boost from Kari, and more importantly, and his dramon destroyers. The other megas didn't have either advantages. Also, as mentioned, its possible that this Machinedramon, created by Yggdrasill, was revived much stronger than previously.
The reason why Meiko survived after the Mysterious Man choked her, is apparently Word of God confirms that if the human dies, then their partner digimon dies too. He held back because otherwise, Meicoomon would have died as a result.
As stated in a comment: Why is Omegamon's new form called Merciful Mode? Meicoomon was suffering. Omegamon was giving her a Mercy Kill, ending her pain.
Some may have questioned the need for Omegamon's name to have been changed to Omnimon, as a common definition for "omega" is "greatest", which certainly describes Omegamon as one of the most powerful Digimon in the franchise. But Our Future shows that Omnimon is as fitting a name for Merciful Mode as Omegamon after all, as "omni" means "all" and OMM is the fusion of all eight protagonist Digimon from Adventure.
The reason the 02 kids were done with first isn't just a Take That! to 02; they were taken out because Imperialdramon Paladin Mode is a Story-Breaker Power. The Omni Sword's ability is to "reset and clear configuration data"; this is what it does to Armageddemon in Diablomon Strikes Back and would have also been an insta-cure to the infection in tri. And while getting rid of Tai and Matt would have had the same effect of taking Paladin Mode out of play, Omnimon by himself was more powerful than Imperialdramon Fighter mode, and was an even match for Alphamon, whereas Imperialdramon was taken out relatively quickly by Alphamon.
The forms the Mysterious Man takes depends on where he is (Human or Digital World) and his subsequent behavior and actions:
In the Human World, he masquerades as Ken/Digimon Emperor. This makes sense because since he is in the Human (real) world, he needs a human (real) body. Ken would be ideal because he was the first evil human in the series and it allows the MM to continue to mess with everyone, making them think Ken is evil again. He never seems to take Gennais form when in the human world. Also, while masquerading as Ken, he treats the events occurring (Ordinemons rampage) as a game and spectacle. This is very similar to Kens original mindset of what Digimon and the Digital World were, specifically that it was all a game for his amusement.
In the Digital World, he takes Gennais form. While in this form, he behaves the exact opposite of how Gennai traditionally behaved. He treats the Digidestined as literal children and shows no respect for them. He constantly berates them instead of giving them advice, while the real Gennai helped as much as he could. He also acts brashly and is very haughty, while the real Gennai was very humble (iirc) and patient).
Unless Ken, Davis, Yolei and Cody were all defeated simultaneously, at least one of them watched their friends (or (eventual) significant other in the case of Ken and Yolei) get cut down right in front of them and were unable to stop it and the others had to live with their last thoughts being about how they failed to protect those same people. This is particularly strong if Ken (who had already had to deal with the deaths of his brother and his Digimon partner in the past) was the last to fall.
Also, where are Veemon, Wormmon, Hawkmon and Armadillomon during all this? And are TK and Kari ever concerned with them?
The fact that the 02 kids must have been missing for at least a year (as that's when the gates to the Digital World closed off spontaneously) before tri. started is horrifying in itself. Yes, they've saved the world before and they've got their Digimon, but they're still kids and they were trapped in a world of monsters with no way to contact their friends and family before their brutal defeat.
Added to this: if Davis, Yolei and Cody were in their right minds during any of this (given the whole Imperialdramon thing, Davis at least is currently Not Himself), they were alone, scared and possibly without access to most of their abilities and those of their Digimon. And now with Not Himself Davis on the scene, Yolei and Cody, neither of whom are good at leading, are alone in the Digital World and at risk for being turned into monsters against their will, with their Digimon dragged along for the ride. Almost makes you feel sorry for them.
Yet anotherFridge Horror regarding the 02 kids. Assuming they're still trapped within the Digital World at the time when it reboots, what the hell would happen to them???
Ken being the Digimon Kaiser again and destroying Primary Village. Not only is this horrific in general, even if Ken is brainwashed or something, all his hard work fixing the damage he did and atoning for his actions, making up for his bad reputation from being the Kaiser in the first place, is basically down the toilet. Harsh.
As of Confession, it's been revealed that the Kaiser isn't Ken, but a Mysterious disguised as both him and Gennai. This begs the question: What the heck happened to the REAL Ken and Gennai!?
Admittedly it's nothing new in Digimon for Leomon being killed again. But consider this time, he was deleted in the human world. Just like Wizardmon, there's no coming back this time.
Partially right. In Loss, the Mysterious Man says that "Because of the reboot, even the Digimon killed as Digi-Eggs or in the real world come back!"
When infected Patamon bit Takeru in Confession, it was quite a surprise. But on the other hand, he evolves from Tokomon, who is infamous for his mouth full of teeth, so it's not a surprise when you realize this may be a natural defense for him aside from Air Shot/Boom Bubble. Then imagine how he'd behave when something's clearly not right.
If the reboot of the Digital World revives every Digimon who died, regardless of where... that would include Digimon like Devimon, or Etemon, or even Myotismon. Oh, Crap!
Possibly not, however, as the evil Digimon (from Devimon up to the Dark Masters) were the result of Apocalymon's influence from beyond the Wall of Fire. With Apocalymon not around (or at least not in a position of influence) after the reboot, those evil Digimon would never have come about (the Dark Masters that do appear seem to be mindless and puppeteered by 'Gennai', implying they're not the originals).
The ending of Part 4, while brief, showed us a possibility that's scary to entertain. What happens when a child were to die or be killed in the Digital World?
In most of the media, Homeostasis, working through people like Hikari, has been the goddess of the Digital World, and a very passive goddess, with it being suggested that she took over the role after Yggdrasil turned evil. As of the Reboot, It seems like Yggdrasil is back in power.
Added to that, could Hikari's corrupted Digivolution be due to Yggdrasil possessing her this time?
Why were the Digimon partners having such a difficult time killing Raguelmon in Coexistence, or at least purifying her? Because if you go back to Adventure, the partners alone weren't enough to kill Apocalymon. Now they were up against a Digimon which is effectively a fusion of Apocalymon and Rasielmon, the latter of which is an angelic Digimon on par with Seraphimon and Ophanimon.
Towards the end of Our Future, Meicoomon is revealed to have backed up all the memories thought lost in the reboot; once unleashed, every Digimon regains their pre-reboot memory. Good right? Well, remember that one Digimon that was brought back is Tapirmon/Bakumon. Who'd just rejected Maki because he didn't remember her, something that broke Maki's spirit entirely and she was swallowed up by the Dark Ocean. Imagine being in his position when he suddenly regains his memories of her.
According to Word of God, if a Chosen Child dies, their partner dies too, hence why the Mysterious Man didn't kill Meiko, as he still needed Meicoomon. Daigo is heavily implied to have died in his Heroic Sacrifice, and while the Reboot may have wiped out his memories, Bearmon will most likely die too now. Made even worse is that Bearmon was originally Baihumon, one of the four Harmonius Ones. Before, there was at least a chance for them becoming the Harmonius Ones again, but now, with Bearmon gone, either Baihumon can never return, or Homeostasis will need to create a new Baihumon.