Having finished it, I didn't think the ending was bad. A little depressing, sure. I don't really mind Shepard's death, or the galaxy losing the mass relays- they made it clear in the epilogue that earth is going back to the stars, it just may have to be on their own terms, without ancient alien advancements speeding it all along. This was intended to be the last game in the trilogy to my knowledge, so I don't see why they are quite relevant.
The Normandy Crew being stranded was a little strange, but my guess is that it is likely due to upcoming DLC dealing with their predicament. When you described the ending to me it sounded surprising, but in action... I don't get the uproar.
I guess on the other hand, some people were mad when tons of folks died, many were left on primitive earth, and the whole fleet that allowed interstellar travel was flown into the sun at the end of Battlestar Galactica too...
$35000 is pocket change in terms of multimillion dollar game developments like ME but I suppose it could influence one of the DLC's down the line.
Everybody good, plenty of slaves for my robot colony?