You dirty old Cynic you. 
Granted. The Story will offer you a lot of Choices with both having positive and negative Outcomes, only measured by your Squadmates Approval. Sadly, this opens more Cans than it closes, forcing the Game to end with only few of them resolved. The Sequel will be cancelled due to the horrid Amount of Cosequences that would have to be considered.
I wish for the Story to be realistic, but not cynical or dark.

Granted. The reapers return in ME:A and completely obliterate us in a matter of hours. We stand no chance against them (because you wanted a realistic game) and the game will therefor only have a bad ending where humanity gets exterminated and turned into a reaper. However, if you play your cards right you can still ensure that the next cycle doesn't get destroyed by the reapers, giving you a somewhat happy ending (assuming the leaders of the next cycle will be less moronic than the leaders of our cycle).
I wish for a dark and gritty game that gives us a realistic depiction of the horrors of space travel and dealing with aliens that are so foreign to us that peaceful cooperation seems almost impossible.
(PS: You should really play The Witcher trilogy if you think what I previously wished for is impossible.)