Yeah, under the new system, just putting one point in a skill ability is pretty much all you need - that alone will eventually allow you to get any 3 of the most powerful skills in that category, which is probably enough. An easy way to fix this is to require higher skill ability levels for the more powerful skills, kind of like the previous beta versions did (i.e. having "Level 1" through "Level 5" skills) - see the thread linked by SGnri above.
