Structure-better structure or bishop pair in the endgame? Does the bishop pair compensate for doubled pawns if there are no rooks to attack with the bishops in the endgame?
More often than not, the Bishop pair will compensate for doubled pawns in an endgame.
Your unopposed bishop would have to be pretty bad (and therefore your overall position) if it's influence did not compensate.

In general doubled-pawns are not that bad if you have active piece play.  Look at the games from the Kasparov-Short world championship match.  Nigel Short repeatedly had doubled crappy looking pawns but because his pieces were active Kasparov was not able to capitalize on their weakness; this fact was well commented at the time.