Things you wish would've happened in the trilogy

Or just having a proper first encounter situation. One that isn't solved by taking a walk through a holiday resort.

That would be a good option. I like Reegar. He had the best red colored armor in the trilogy

That Kaidan and Ashley had actually been two different people in ME2 and the beginning of ME3 instead of Kaidashley.

It just irritates me that Kaidan forgets that he's a biotic. All the scenes that he's interchangeable with Ashley, were written solely with Ashley in mind. I just wish that even if they had the same events happen that Kaidan would act like Kaidan (like on Horizon instead of shooting at the seekers swarms he would have used throw or something to try to push them away even if it still failed to do anything). Once the coup happens on the Citadel in 3 and they join the party they start being two separate people again. As evidenced by how Kaidan starts questioning his own thoughts about people who joined Cerberus after the Ex-Cerberus Scientists mission, and Ashley doesn't.

I rarely romance Kaidan, but he is one of my favorite characters. And it's just frustrating that for a game and a half his personality is subverted to be just like another character.

I wish that the super enthusiastic human C-Sec agent you meet in the Wards in ME1 was the Bailey of ME2. Granted, it would mean that "Bailey" was less grumpy, but it would have given more meaning to the first real interaction Shepard has on the Citadel.

It was pretty bad how he got his ass handed to him by Eva, when he could have easily used his biotics in that scene. Their dialogue is copy/paste the same during Mars, though, with slight variations so you remember who you're talking to.

Adams, Dr.Chakwas, Ken and Gabby added in the memorial scene

Yea, looking back, you realize how disconnected ME2 was to the whole trilogy. When it came out, it felt great since the gameplay and characters were top notch, even if the story was a little on the short-side. There definitely should have been more Reaper-threat build up. Ya know, we could have investigated some more plot-items through Cerberus.

I know of people who think ME2 is the best but still call ME3 "ME1, part 2".  To me, that's acknowledgment that the story was derailed and got back on track in ME3.  I think it might have worked better if the Reapers came as a consequence of your actions with the Collectors.  Imagine if accessing the Omega 4 relay somehow set things in motion because the Reapers now knew that Shepard had an IFF that could also potentially allow access to their base in dark space.  Something more concrete to the main plot of ME2 rather than the plot of an ME2 dlc.

In a world where BioWare had limitless resources:

1. Shepard immediately takes the Normandy and goes to the Alliance, handing over all the evidence he has about the Collectors. Shepard never works for Cerberus at any point. Miranda and Jacob may or may not be allowed to remain but the rest of the squad work for Cerberus. Consequently, the VS joins as the new XO.
2. Going into ME3, Shepard has the option to remain with Cerberus or return to the Alliance. Going with Cerberus cuts off the Citadel as a hub until the coup, at which point Cerberus takes control. Once again, Shepard holds the fate of the Council in his hands and can choose to eliminate all but the human councilor. Also, going the route means that instead of fighting Cerberus forces everywhere we fight Council/Alliance forces everywhere. Maybe we even learn the Council is indoctrinated and that's why they've ignored the Reaper threat. If Shepard goes with the Alliance, the game is pretty much the same as what we have. This allows Shepard's Collector Base choice to hold much greater weight.

I believe there is an element of that in the actual game? If you have very low EMS and destroyed the base, Destroy is the only option; if you kept the base, Control is the only option?

I like your suggestion, it would make the decision at the end of ME2 more significant; and it also fits with my own personal belief that Control is the most Renegade of the ME3 choices.