I have a bunch of non-ending related questions:
1. What happens if you don't do overlord and then save Grissom academy? Do you just not interact with Archer? Do you still get the guns/room full of ammo?
2. What if I destroyed Maelon's data in ME2? Does that affect the genophage stuff?
3. Related: is there any way to save Mordin?
4. Any way to save Samara? Thane?
5. Is there a way to get Kaiden back on the Normandy? I didn't actually want him, but I'm curious if that is possible.
6. Is there any interesting choice in the Miranda quest? I don't see how anything I did helped her or changed anything.
7. Any consequences for reprogramming rather than killing the heretic geth in ME2? I killed them.
8. Re: Rannoch: Does it matter what order you do the missions in? I did the Reaper base last and I'm wondering if you can still do the others if you choose that one.
9. Did I miss something regarding the council? I made them all human in ME1 and they ended up being mixed again in Me3.
1. I did overlord and my Renegade Shepard didn't take the guy from Cerberus, so no, he wasn't at the Grissom Academy and as such I didn't get to go into the extra room on the side.
2. Eve dies if you didn't save the data, Mordin will talk about the condition she is in and how she is deteriorating and could have been saved had you not deleted the data.
3. As far as I know the only way to not have Mordin give up his life or have to kill him is if you shot Wrex in ME1 and as such can convince Mordin to wait on the cure till someone better than Wreav comes along.
4. You can save Samara from shooting herself with a Paragon interrupt, I don't know what you need to have done in the games for it to show up mind.
Thane will always die if he survived ME2.
5. Yes, Kaiden/Ashley can be asked to come back after the Priority: Citadel mission, I'm not sure if there is as certain something you have to do, but it just came up in a conversation afterwards.
6. What do you mean by interesting choice? if you don't warn her about cereal ninja or something she ends up getting killed I think, if she didn't survive ME2 the mission happens just without her and with her sister or something.
7. Reprogramming the Geth make it harder to form an alliance between the Quarians and the Geth, while the Paragon option in ME2 it in fact makes the Geth stronger and as such harder to bring about a truce between them.
There is a hidden point system behind Geth/Quarian things going on, you need a certain amount from ME2 and ME3 to be able to choose the peace option.
8. Not just Rannoch im sure, but if you go straight to the Priority Mission you will miss out on the side mission on the planet, pretty sure you have to do all the side Rannoch missions before the main one, same for Tuchunka.
9. You didn't miss anything story wise, just Bioware replacing the default Council with another so it gels with the story and they didn't have to put in the work of making the story continue without each race.