Steering this thread in "that direction" is as much your fault as anyones. In the interest of comity, however, I'll provide you with a few things I'd have liked to see differently.
-less auto conversation and more actual conversation among crew members, both with each other and Shep.
-perhaps having a fracturing of alliances that impact the game near the end or the immediate aftermath (say, maybe the alliance having to fight the Krogan or Geth, while still combating the Reapers, depending on the outcome of those missions).
-Maybe, unbeknownst to Miranda, TIM actually had a switch put into Shep that allowed him to seize control and manipulate Shep into turning the Reaper assests over to him (meaning that, yes, TIM somehow manages to avoid complete indoctrination).
-getting rid of the War Assets feature as well as actually finishing the damn game and limiting dlc to mostly cosmetic changes (weapons, outfits, etc..)
-game shouldn't have come to a close so soon after getting to earth. More combat (perhaps where you could see the effects of fractured alliances) planetside.
-EA not obsessing about costs so much when they had an eager and built in audience willing to throw down mucho $$$ to complete their franchise.
Just a few ideas.