I really don't see how people think this is a 'bad' ending.
What did you want to happen? For Heller to sit on the top of a building in New York singing Christmas carols?
I enjoyed the ending. The wife saying "What do we do now?" is a perfect ending. It's not made to be all rosy and happy. It's a bleak city, the virus caused a lot of damage.
I haven't played ME3 so I can't comment on that, but P2 is hardly a bad ending. But, people aren't happy unless they are bitching about something - so bitch away. ;-)