Well, to me this just doesn't make any sense. If I have never even equipped a two-handed weapon before, why can I place a perk in the two-handed skill and become better with those weapons?
So my idea is that, when you level up, the only skills you can place a perk in are the ones that you actually improved during that level-up. So if you didn't swing a two-handed weapon during your last level, then you can't place a perk in that tree.
This would give you more of a "class" feeling, because only the skills you really used would be able to become powerful for you.
Thoughts?