Frogboy has said that he sees mixing ideologies as a feature and not a problem. We all have mixed ideologies so I don't have a problem with that.
The only problem I have with the Ideology feature is that it is too dependent on colonization and it slows down drastically after the rush. The planet improvements don't provide enough points to keep it moving for me. If the Missionary gives me .1 points per turn and I build 30 of them, that give me 3 points per turn, after they are built, which can take a long time. If they were all built instantly that would probably give you an ideology choice every 30 turns or so or 10 times in a 300 turn game. They don't get built instantly so I am figuring you will do well to get 5 ideology picks form the Missionary per game.
There are also a few quirks that bug me a little. If your race has the trait that excludes ship yard distance decay, one of the pragmatic bonuses is worthless. I am also having a problem understanding how the last Builder bonus (the new one) in the Pragmatic tree stacks with the previous bonuses. One of the faction traits gives you 2 build points when you build a star base, one of the pragmatic Builder bonuses gives you 2 build points on every module. What does the last Builder bonus do? I can't see where it does anything in my game. When you send a constructor to a base after you get the first pragmatic bonus, you get 2 build points. The last pragmatic bonus in the tree sounds like it should double that. I might be misunderstanding the doubling part but like I say, I notice no change after selecting that bonus.