I'm kind of split between Franklin and Trevor.
With Franklin, although I don't dislike him, I feel like he becomes the "odd man out" in the gang when the game starts focusing more on Michael and Trevor's relationship, and as such, it would be interesting to see what killing him off would do to the other two.
With Trevor, it's kind of complicated. I would kill him because I don't like him, but I have some problems with how it was done in the game:
1. Trevor's death doesn't feel "karmic". As much as I like Michael, you did get the sense that he reaped what he sowed in Ending B. Not so with Trevor; he just got betrayed a second time.
2. Ending A goes by very quickly and doesn't really resolve the existing plotlines.
So in conclusion, I'd kill Trevor because I don't like him (assumuing it was done a little differently than it was), but I wouldn't mind seeing what would happen if Franklin got killed, because the game began with Michael and Trevor, and it'd be interesting to see what happened if it ended with them.