Might not be the most appropriate topic to post this in, but:
On my transition from ME1 to ME2, there was something that ticked me off. In ME1, Wrex had been my squadmate from the moment I recruited him. He went with me everywhere. Then in ME2, I got Grunt from Okeer. There was some 'discussion' about it being a Krogan and everything.
I would love it if the game recongnised that I had a Krogan in my squad all the time in ME1, and react as such when I try to recruit another Krogan. Hell, I would've been extremely happy if Shepard had said something along the lines of: "Wrex has helped me out many times, that's why I want this Krogan", or something like that. A single line would be enough. No need for big consequences or changes, just a simple recognition of what has happened before.
Can't even be seriously hard to implement. All you'd need is a few checks in the save about who was a squadmate at what time during what mission. It's tracked who is your favourite squadmember for the ending of ME3 (it decides who exits the Normady with Joker), so I'm not coming up with something revolutionary here.