My current gaming group recently converted an ongoing game into Pathfinder, with minor changes like the skills at first and then apparently going whole-hog. I have been away at school while they made the switch, however, so in about two weeks I'll find out how it is affecting the gameplay. Already, converting my character has been a slight hassle, since it uses some things which were specifically included in the PFCR, and some things which are not. Though, some things do seem somewhat better off from the switch, like the recent wizard levels I added.
Eventually this is going to end up a game full of mangled gaming rules, including Pathfinder RPG, D&D 3.5, and even the Epic rules, so I'm somewhat worried it's going to get overly convoluted, though we'll see.
Mostly, it seems the group is treating it more like another set of houserules on top of 3.5, including what works within the campaign and excluding whatever doesn't.