This skill system just doesn't feel at all nice to use. You've limited our choice to three per level but we still have to worry about the entire tree if we want to achieve anything approaching usable/fit for purpose(s) for a high level creep.
I've said it before and i'll say it again. If we could pick each skill and then have to wait n levels before being able to level it up we would end up with a pyramid of choice not a threesome of suck. For the more powerful skills you can require that we are at least level n before we can pick it at all.
The end result is much the same; you force us to generalise our power creeps but you put the power in the hands of the players. This is in addition to giving us a system that does not feel awful to use and plan around.
edit: another thought is that with the current system you cannot merely add another skill into the tree later on; or even move them about post launch. You need to re-work the entire tree which has the potential to completely break builds & code.
tl dr; This system is working against us, not for us. We have to plan around it, not with.