Well, power issues aside, something I dislike is that they strongy encourage playing against your role. Not that that's inherently bad - but let's see:
E.g. Travelling Missionary gives you an extra language, Religion as class skill and a +2 bonus to Religion. And it's a good background for clerics who already have Religion as class skill.
These skill-centric backgrounds actually encourage you to take a background not fitting your class to get the most out of it.
Worse, if you try to play a straight up character and select a background first, then select a class modelling the background well (like Travelling Missionary as background and cleric as class), you fell like you've "wasted" part of your background.
Now, I understand that it's not a real power issue (since you don't get extra skills, just more choice), but it just feels weird.
Same for similar backgrounds, like Magic Scholar, Silent Hunter, Explorer/Guide, Con Artist, Cloistered Priest and some others.
Cheers, LT.