For me it's not about a happy ending, it's that all in all the ending doesn't match the flow of the game, and all the endings are the same.
So the game is literally built around two premises. One that it's better to burn out, then to fade away. To die young and make a difference and be remembered, or to simply die of old age. Second, and lesser, the quandry of the soul. The second point is covered in the ending. The first one not so much.
So V dying young, not a bad deal given the premise, except for the fact that she didn't burn out, she really accomplished nothing, all in all, other then maybe making a few friends and effecting maybe 10 peoples lives, she did nothing.
Which for real life is realistic, but for a movie it kind of sucks. Hell Bladerunner showed that Decker went on a life changing journey and discovered more about himself. You kind of get hints of that with V, but it's so muted, so hidden behind Johnny, that it seems neutered.
So you get to ride off into the sunset, or stay in town, and do nothing, die of young age and be forgotten, which is exactly the opposite of making a difference and being remembered.
Hell ME3's ending wasn't happy, but you made a difference. I don't need happy, I need endings which follow the premise of the game, and aren't 7 endings all the same (V/Johnny dies) with minor differences (you stay in town/ride away).