Here are the ones I've noticed -
* Muffled Movement
A great perk for anyone using armor, but unfortunately worthless to unarmored builds, yet they're required to sink a perk into it to progress through sneak's main line of perks. This perk should've been split from the main line so armored characters can choose it, but unarmored characters can skip it.
* Deadly Aim
Backstab is required for it, yet backstab is something most characters aren't even going to want if they're going for deadly aim. I understand making it too easy for archers to get might make it too much of a no-brainer perk, but it could be linked to talents that still actually do something for them.
* Fist of Steel
..........................................enough said.
* Smithing
I can't really even narrow it down to a single perk, but half the tree is utterly worthless end game. It's unfortunate for those who like the aesthetic of glass armor over dragon, but they're stuck with the 3rd tier of weapons unless they want to spend several extra perks to reach Daedric or Ebony weapons on the other side. They should've linked glass with daedric and advanced armors with ebony and so on, so that people going the glass side don't get such a bad deal.
* Fire/Frost/Storm Enchanter
These should just not be in a line, a Dunmer for example might want just the frost resist, but has to take fire which is a bit redundant for a Dunmer. A Nord could happily skip frost to take fire - fire and frost are obviously the two most important - and essentially gets an extra perk advantage on any Dunmer due to the layout of this tree.