At the end, Shepard is given three choices. Paragon: Save the asari dreadnought. Renegade: Screw the Council over. Neutral: Focus fire on Sovereign, thus killing the asari dreadnought anyway. The neutral choice still gives you renegade points, because not taking action when you can is still JUST AS BAD.
The loading screens in Mass Effect 1 that depict the Normandy traveling between systems - the ones that show it using its built-in FTL drive with the red light heading "toward" the Normandy and the blue light heading "away" from it – seem like just a pretty cool effect. However, if you reread the Codex's entry on FTL drives and their appearance that you realize the light "approaching" the Normandy was being red-shifted by the mass effect field (as to an observer inside the mass effect field, everything outside is red-shifted), and the light moving away from it was being blue shifted (as an observer outside the field would see everything within the field as blue-shifted), exactly as it was described in the Codex. The sheer level of detail and dedication to internal consistency in the game's very loading screens is amazing.
Manuel from Eden Prime may seem crazy at first but looking back, everything that he babbled about was actually true. He was probably exposed to the beacon just before the attack. The doctor describes him as 'always a bit unstable', but maybe this is what happens to a 'lesser mind', as Liara put it.
Remember that song that played every time you died? That one that you began to associate with death and eventually hated? Well, it's Saren's theme song. Meaning that the game developers have been conditioning you the entire game to hate him. Shepard was the only one that could stop Saren. Now s/he's dead and the Game Over music is Saren gloating. The menu music? That's Vigil's Theme.
The only time you hear two elcor speaking directly to each other is in Mass Effect in the elcor ambassador's office. Careful listeners will notice they do not preface their conversation with their emotions. Of course, this is because they can detect the minor physical and pheromone changes of each other, and have no need to express them verbally.
After the Feros debriefing you can chat with the Citadel Council, and if you're following the Paragon conversation paths, a chilling bit of foreshadowing occurs. After the jerkwad turian councilor calls you out for protecting the human colony, the salarian says something along the lines of "just remember, Commander, sometimes you have to be willing to make sacrifices to get the mission done." He probably wasn't expecting that you can choose to do exactly that to him and his fellow councilors as one of your final decisions.
In the first game Sovereign refers to the Citadel and the mass relays as "the legacy of my kind." It's not the legacy the Reapers left behind. It's the legacy they inherited.
The Colonist and Sole Survivor origin stories give you both paragon and renegade points at the start. Initially, this makes no sense, since, after all, how is everyone around you dying related to your morality? Then you realize: the experiences were so traumatic that Shepard's psyche was partially fragmented. How does the game show this inner fragmentation? It gives you both good and bad points toward your morality. It's also because those two backgrounds are morally neutral when compared to Spacer/War Hero (Paragon) and Earthborn/Ruthless (Renegade). Colonist Shepard was raised by loving parents (Paragon), but probably had to do some dirty things to survive (Renegade). It's implied that Sole Survivor Shepard tried to help the other marines (Paragon), but eventually gave up and decided it was every man for himself (Renegade).
During the endgame of ME1, Saren is marching into the Council chambers and takes a potshot at one of the Keepers that maintain the station. Why did he do that, other than generally being a grouch? Sovereign was frustrated that the Keepers had not functioned as they were designed to, and was taking it out on them via Saren.
Your squadmates in the first game each represent one of the classes: Ashley is a Soldier (all combat), Kaidan is a Sentinel (tech/biotic), Wrex is a Vanguard (combat/biotic), Garrus is an Infiltrator (combat/tech), Tali is an Engineer (all tech), and Liara is an Adept (all biotic). There are some differences, but the basics are there. Further, the only squadmates whose skills are identical to Shepard's are Ashley and Kaidan, because they got their training from the same place Shepard did. Everyone else's training is slightly different, and for good reason:
Garrus and Wrex are trained in Assault Rifles, which are normally only available to Shepard as a Soldier. This is because in both of their societies, Garrus and Wrex were trained as soldiers. Also, without this training, Assault Rifles would be near-useless to any Shepard besides a Soldier. This way, you can at least hand them off to a squadmate.
Wrex is a tank on two feet, so naturally he has access to both Immunity and Barrier, but not Adrenaline Rush like Vanguard Shepard would have
Tali can use shotguns because of her military training on the flotilla (which would favor close-quarters combat because they typically have to fight through ship corridors), but because she's a starship mechanic and not a doctor, she doesn't get the Medicine skill you'd expect Engineer Shepard to have.
Liara is the only squadmate with no military training at all, so she doesn't have access to any of the weapon skills (even Adept Shepard at least has pistol training). And the Electronics skill she picks up instead is a hint towards her future occupation as the Shadow Broker. The Electronics skill also ties to the fact that she's a scientist/archeologist - and spending almost fifty years on remote dig sites deciphering complex Prothean artifacts helped too.
In Retribution, when Grayson is resisting against the Reapers' control, they subtly shift his thought processes so that he decides that best course of action is to find Kahlee, which is what the Reapers want anyway. Now, go back to Mass Effect 1, where Saren and Shepard are fighting at the base on Virmire. Shepard begins to instill doubts in Saren's mind, but then Saren suddenly becomes angry, declaring that his plan will save countless lives and that Shepard's actions would undo his work, and then he attacks in a rage. Sovereign was doing the same thing to Saren that the Reapers did to Grayson: subtly shifted his thought processes so that he would conclude that Shepard was going to "undo his work" and then attack him/her, instead of stopping to listen.
Try starting a new game of the original Mass Effect and pay close attention to what Lt. Jenkins says... everything he says is foreshadowing the upcoming events. One of the things he says is that if a Spectre goes rogue, the Council will send another Spectre to deal with him. Chakwas dismisses this as romantic fantasy from a naive kid who watches too many vids. Turns out, that's exactly what does happen: Saren goes rogue, and Shepard is sent to take him down.
A big deal is made of how unbalanced the battle was between the Citadel Fleet and the Alliance 5th Fleet against Sovereign. A key detail that is easy to miss though: Sovereign was a full-up dreadnought, and a very powerful one of those at that, while all of the Citadel and Alliance ships (save for the Destiny Ascension, which was not fighting under the conditions she was for: Long range slugfests) were cruisers or smaller. Of course it would be a slaughter for the defenders, especially if they were also having to deal with the geth ships.
Sovereign is a sovereign derived from a social contract made by its constituent intelligences, as detailed in Jean-Jacques Rousseau's The Social Contract.
The relationships with Kaidan and Ashley seem very reserved before Udina grounds the Normandy and the crew heads to Ilos. There's plenty of flirting and questions about the relationship, but really no signs of physical affection. So what's going on here? Shepard, Kaidan, and Ashley are all Alliance soldiers on an Alliance ship. Shepard is Ashley/Kaidan's commanding officer and fooling around with your subordinates while on a mission is a HUGE military no-no. They can talk about where they'll take their relationship when the mission is finished, but are holding back for now due to protocol. It is only after the council screws Shepard over and the team is willing to sacrifice everything to go after Saren that Shepard and his/her love interest essentially decide "Screw it, we might not have another chance." and take things to the next level. With Ashley, add to it that Shepard is an officer and Ash is a noncom. Enlisted/officer relationships are equally frowned-upon.
At first, Saren's plan looks insanely stupid. A Spectre with virtually unlimited authority could walk right into Eden Prime, use the beacon, and then sabotage it to make it look like the humans couldn't handle the advanced tech properly. Instead, he grabs both the Villain Ball and the Idiot Ball, organizes a massive geth assault and reveals Sovereign, and while it would have been deemed a wholly geth assault had the Normandy and Nihlus and Shepard not been around, it makes sense when you factor in that it's Sovereign's plan, not Saren's. Sovereign doesn't give a flying Reaper fart in space about Saren's Spectre connections or being subtle at this point (and with good reason, he's possibly facing a You Have Failed Me from Harbinger for fucking up so many times to open the Citadel relay), and they would actually benefit from getting organics up and in a tizzy. With the forces of the Citadel species out and about the galaxy guarding against another geth attack, Sovereign/Saren's forces could more easily break through at the Citadel. Also, since Saren is trying to resist Sovereign's indoctrination it's quite possible he's deliberately grasping the Idiot Ball and the Villain Ball, hoping that someone will discover his plot and stop him. Saren's plan ends up setting the Reaper invasion back years, and even if he had succeeded, the council races would have gotten a good clear look at Sovereign.
When the Citadel council (at this point still believing the conduit to be the entry point for any invasion rather than the Citadel itself) decides to deploy fleets to guard every relay between the Citadel and the Mu Relay, they are completely surprised by Sovereign and the geth fleet, which completely bypass these lines of defense. How Sovereign was able to do this was a complete mystery, but a significant clue comes in a DLC in the 2nd game: the Alpha relay. This relay has hidden capabilities that allow it to send ships to any other relay over half of the network. And since it's in batarian space, nobody allied with the Citadel would have known about it.
When you're at the Peak 15 research labs, you can trigger the neutron purge early and wipe out the Rachni. If you do this, when you come back you'll find Captain Ventralis and his mercenaries, who tell you that they've got new orders from Benezia, and start shooting. He even apologizes about having to do it, too. After wiping them out, if you look around, you'll find all the scientists and workers are gone. All of them. Everywhere. And there's nowhere for them to have gone... which leads to the rather frightening yet logical conclusion: Ventralis and his men didn't just have orders to kill you, they were ordered to wipe out everyone at the research station. Confirmed when you talk to Han Olar (the traumatized volus scientist) after saving him from Benezia's forces.
That "Rogue VI" on Luna that you destroy was actually EDI before she was augmented with Reaper tech. The same EDI who is standing right next to you when this is revealed. Good thing she doesn't seem to hold a grudge about it. This gets further awkward when revisiting the beginning of Mass Effect 2: when EDI appears the Renegade option is to act hostile towards her, which prompts Miranda to point out to EDI that Shepard has had bad experiences with AIs... and brings up the Luna VI (aka EDI) as an example.
It's very easy to overlook, but if you read up on the information regarding the "Rogue VI", you'll find that someone DELIBERATELY tampered with it to cause it to go crazy. There's no investigation as to who exactly did it, but in Mass Effect 1, there's a short sentence mentioning how there were signs of tampering with it's controls before it started killing people. When you think about the above point from Mass Effect 2, it was nowhere stated that the Luna VI was an AI, yet Miranda directly refers to it as one. How could she have known if it was an AI? Easy: she's working for Cerberus, who tampered with the VI to make it an AI.
On the subject of the Rogue VI on Luna, after you defeat it you get a popup explaining that Shepard's comm gets filled with white noise that was converted to binary. If you then further convert this binary into ASCII, it spells out the word "HELP". Especially horrifying if it was an AI as the above theory posits; it was sentient, it asked for help, for mercy... but you killed it anyway.
After Saren shoots and kills Nihlus, we see him brooding in his chair and looking pretty sullen before he learns that Shepard thwarted his attack — so he was acting pretty broody even though he thought he'd succeeded. He seemed pretty much a sociopath when he killed Nihlus, and he starts chucking things around in an obvious tantrum, and yet for the rest of the game he seems to be a pretty calm, if determined person, right up until the end when he shoots that keeper. So that seemed a little strangely out of character. Later on, we see that when he's indoctrinated, his eyes glow blue, and they stop glowing when he fights it. Replay the game, get to the scene where he meets Nihlus, and you'll see that his eyes glow blue when he shoots Nihlus. It especially further explains why he sounds desperate and even a bit pleading when he talks about researching and fighting indoctrination.
A bit of Fridge Sadness. More than once, there are hints that Ashley and Kaidan were attracted to each other, especially if Shepard is romancing Liara instead. Obviously, this is a doomed ship. On Virmire they were both telling you to save the other one. They weren't just being heroic - they were trying to save the person they loved (or, at least, had feelings for)!
Buried away in the Codex is the fact that the genophage does NOT affect krogan fertility rates - it affects fetal viability instead. The previously-fecund krogan aren't simply subject to low birth rates - they are subject to entire litters of stillborn babies.
Several assignments can become just this when you think about them for a little longer:
The MS Worthington is completely empty except for brain-dead Jacob and his psychotic biotic girlfriend Julia, meaning that sometime between killing the captain and Shepard's arrival Julia killed the entire crew.
The missing survey team on Trebin were all converted into husks and - according to a data log - had previously discovered an alien artifact that turned them into mindless machine worshipers. When you enter the mine where you find the survey team, you realize that the only alien artifact in the room is this glowing orb inside a mechanical claw that looks just like the "geth temple" on Feros and remarkably similar to Reaper Tech. Which means that: 1) the survey team became indoctrinated and essentially huskified itself, and 2) the geth on Feros may have been indoctrinated as well, instead of being willing worshipers. What makes this even worse is that Shepard and his crew say that they have heard about such devices/artifacts before, meaning indoctrination has been around a lot longer than believed.