while I'm not keen on the federation as they seem to follow a rather typical wilsonian philosophy (prime directive or no). While the federation talks a good game, to me, it just seems like a bunch of humans pushing their view points on other worlds and cultures. However, I can't say I'm fond of the romulans or the klingons either. Those two present rather strawman representations of nationalism and militarism.
IMO, this is one of the things that makes the ST universe unappealing, political ideologies are just too simplified and there's an un-natural delineation when it comes to militaristic versus pacifist thinking.