There are trees that are way too useful (Smithing) and trees that are way too useless (Lockpicking). Similarly, there are trees that have a lot crammed in them (sneak has some acrobatics in it, heavy armor unarmed) and others that are stretched too thin (like lockpicking and pickpocketing). They could easily have organised it better (Pickpocket and lockpicking should honestly be in the same "thievery" tree, acrobatics/athletic/unarmed should be in another one etc Most trees are fine in that aspect though)
Also, the fact that most tree have a big universal % at the bottom is not bad, but it certainly is... uninspired. Plus it kinda makes the trees a bit more than simple perk trees - not bad, again, but not really ideal either.
Imho, they should take out those %s in the tree bases, along with the cost reductions in magic trees, and replace them with more specific perk, such as the crit on swords or the reflect in heav armors. And tie that percentage with the skill level (something like +1-1.5% rating per skill level, instead of the 0-0.5% we have now). Wouldn't necessarily make it better, but it would most probably make it more interesting. It would also allow for the better character customisation that many feel this game lacks in comparison to real RPGs.

), Odd Hermit can correct me if I'm wrong, but I don't think he's complaining that those perks don't do anything(+skill effectiveness obviously does something) but that they are things that should've been part of the skill themselves and just stripped out of the skill and made into perks so Beth could go around bragging about how many perks they have like they did a lot in the PR frenzy before Skyrim was released.