You sound like a hard guy to please... you want more stuff (mini-games) but you want less stuff (inventory system/stores)

I agree, I'd like to be able to sell the mods & guns I don't use in order to afford ones that I actually want, but I don't see how the mod system is "clumsy". Its definitely more streamlined than ME1, and a massive step up from ME2 which went completely backwards and dumbed it down by removing a huge chunk of the RPG element.
The side missions are still there as well, so the meaningful content is still very much in play and hasn't been cut out, just the minigames. I mean, I guess they could have put an old-school ME1/2 lock somewhere on the citadel to make you happy

I do feel like the scope of the missions is too confined at this point in my game. I feel like I'm still waiting for the galaxy map to open up, I hope that happens soon.