Quite frankly, I wish ME3 was a little more like ME2, such as... (SPOILERS!!!!)...
Having more than six squadmates max to pick from. Miranda and Jacob's cameos wouldn't be completely pointless if you could actually recruit them to join you on the Normandy, and I don't see why Jack couldn't join you if Tali, who is now an Admiral trying to reclaim her homeworld in ME3, can. And the ME3 squad desperately needed a Krogan powerhouse, IMO.
The planet scanning you do occasionally unlocks a secret mission... which would break up the boredom of "someone on the Citadel needs something, you then wander around the Reaper occupied star systems to get them, and then bring it to them". I mean, I think going to the Elcor homeworld to actually save them as apposed to just scanning their planet and telling their ambassador "it's done" would've been more fun, but maybe that's just me. I appreciate the lack of tedious mineral mining mini-games, but a lot more of the "War Assets" obtained through planet scanning/probing would've been funner with actual missions.
The journal you use to track your side missions actually UPDATES and lets you track your progress, rather than staying completely static until you finish it. The first two games gets this right, the third one completely ****s it up, imo.
More mission variety... I know ME3 has a more war centric storyline, so the heavy focus on combat does make sense, but what I love about ME2 is that you get to do more than just shoot stuff. You get to also go on a stakeout (Thane's loyalty mission), go clubbing and pick up a chick and lure her into a trap (Samara's loyalty mission), and even play lawyer (Tali's loyalty mission). A little more of that in ME3 would've been nice.
And finally... and ending that doesn't suck donkey balls. ME1, you stop Sovereign and Saren and save the Citadel (and even it's council if you so choose). ME2 gave you the possibility of getting EVERYONE out of a *suicide mission* ALIVE (or in the worst case scenario, EVERYBODY DIES). In ME3, the fate of the entire galaxy is reduced to an annoying child popping up in the last ten minutes to spout nonsensical ******** (yeah, organics and synthetics will always be at war, even though I ended a organic/synthetic race war and got both sides to work together... yeah, okay) without the ability to argue back with logic (the Reapers are not the solution to the problem, they ARE the problem, what you are doing is wrong, now GO AWAY and stop killing us), and then he gives you three unsatisfying choices to resolve the conflict (all of which result in the same explosion, just with different colors). Not exactly how I would finish off a trilogy, but that's me.