ME3 would have been much improved with:
-Collectors for a few missions
-Geth with at least a couple more missions
-Cerberus with a few less missions
-Ideally, more uniquely skinned indoctrinated forces units/groups scattered throughout the story/levels
Reaper units needed a bit more variety to reflect the impact they were having on species, and Cerberus was significantly more of a presence than they should have been. I'd have appreciated at least a little less 'muahaha evil enemy to spend 1/2 or more of the game against' and more 'wow these guys are screwed up and I have to fight some of them but maybe they're onto something?' (that really only happened in a couple missions like Sanctuary).
So basically I'd have loved 5ish factions: Husks (ruled by individual Reapers), Collectors (ruled by Harbinger), Cerberus (ruled by TIM), Geth (ruled by individual Reapers), and 'Mercs' (indoctrinated groups that mostly worked the same, like a mix of the merc band/SB agents/etc compositions of ME2, but often look different).
Reskinning is nice when used intelligently. Even Geth could have been reskinned/reanimated into (but largely have the same rules as) the Loki (upgraded?) such mechs.
I'm sure a lot of this is development, design, and hardware limitations though. Limitations I sure as hell hope aren't nearly as present in MEA.
ME2 combat is the most 'gamey' (Gear of War everywhere), and ME3 improved somewhat in that regard, but combat in ME3 was also 'simplified'. This IS very likely tied to making multiplayer work, though even if that's the case, we never get an admission of this from current Bioware employees lol. Hopefully now that they've tried out MP, they can move on this and expand; this is the bright side of Bioware's experimentation - they are inept at first attempts, but eventually seem to succeed better than most games around. That's at least my hope with the 'open world exploration' news stuff started with DAI as well, haha.
But anyway, yeah, I'd have liked less Cerberus, more varied Reapers, Collectors in the main game and mattering (I keep feeling like they were intended but cut at some point), Geth getting a wee bit more love, and ideally more involvement with directly fighting various indoctrinated but generic-in-fights forces. Just the idea of facing civilian-innocents-turned-traitors sends chills down my back, but Bioware I guess was more comfortable with giving us faceless mooks everywhere.