After one play through.
1) Make it feel more like an RPG again. Character upgrades do not an RPG make, dialog branches were good but game felt empty. Take a look at everything you've made before at Bioware, this is a hollow game compared to them. Don't get me wrong it was a okay game but I'm still in shock as it feels like a bit of a let down. Dragon Age I'll still play, want to see the world evolve differently. Felt much more part of something. Even Mass Effect 1 I played it 8 times through, this feels stunted as an RPG. You could have made things simpler but not have gone as far. Heck make it a difficulty level thing. This didn't feel like a sequel. Felt like a spin off. like Baldur's Gate Dark Alliance was to Baldur's Gate.
2) Bring back more of the inventory options. Don't need to go back but this is WAY too far. Felt like Rainbow 6 Vegas 2 with the armour options.
3) Make it feel big again. This game felt smaller. really small. In the last game there was always one planet per system to land on. At least would have been nice to actually go to every planet you were previously on. Really felt small. Should be more. I liked this resource searching better but driving around wasn't bad. Scope wasn't there. Even the levels were tight and controlled. Should be open world not one hallway after another. Take Star Wars : Force Unleashed, still boxed players in but much more open, expansive, felt grand. This was like Modern Warfare tight controlled.
4) Continuity. So somehow in the 2 years guns run out of ammo (overheated guns would just cool). People forget you, Liara dialog sucked didn't really react compared to what I expected. Post end game most people still thought they were Cerebus. Notes of the past seemed hollow, would have been good to Call my mom in the game, I mean I know I'm saving the universe and work with the bad guys but man she'll be really mad when I talk to her in the next game. Even the character powers seemed weaker. Missed that your character couldn't hack everything needed a real team not jack of all trades.
5) Squad interaction needs to be better. Bringing Garrus to Krogan homeworld should have them yell at each other, even the first game had this dialog. I'm mean I took the Geth on the Citadel and NOTHING, not one person says anything. Just goes along. It hollow the game.
PS, Loved the Space Hamster, if you could have him called Boo and be able to send him into a parallel dimension that would close the circle nicely.