Those that keep replying with "nope, the perks are great" are only focusing on those that they've found a use for. And by "use" I mean "useful" as in not so situationally based that it rarely ever does anything but eat up a perk point.
Yes, the design of the perks is incredibly lazy. Most of those that actually help are in fact, just more numbers. At least half of most of the trees are just useless filler (see: any of the Novice/Adept/Master etc perks that bloat the trees with cost reduction) and prereqs for the select few useful perks. The only truly "fleshed out" trees would be one-handed, two-handed, Archery, Smithing, Heavy armor, light armor, block and sneak. All of the rest have some useful perks here and there, but are filled with crap too. Some trees such as Restoration and Lockpicking are complete garbage all around.
Hell the entire perk/skill system was poorly thought out. It is fine to have a system where you get 1 perk per level, quite a few systems do it. The thing is those games are not based around leveling via improving skills and generally most of your power comes from the leveling. The problem for skyrim is your skills do virtually nothing. Yes, yes you do more damage, you soak more damage etc., but it is a 40% swing of weapon damage from 15 to 100 skill, that is about a 1/3rd or the power you get from the perks. Without perking things in many cases your skill is pretty much useless, go ahead and hack away on that 3,000HP dragon with a 20 damage attacks I am sure it will be fun. Heck there is nothing wrong with having the perks give the majority of the power, the problem arises when you combine it with a a perk a level system and the level via improving skills system. You just created a system of pointless grinding which should pretty much never be a design goal outside of MMO's where they are trying to keep you around for years so time wasters are valuable to them.
Basically given the ES leveling system if they wanted the perks to provide virtually all the power then they should have gave out a perk every X skill points in a skill and it would have to apply to the skill raised by X, and make sure there are enough perks so people have to choose and will be able to have different choices on multiple playthroughs. So like every 10 points in marksman you get a marksman perk, but since there are 30 perks the 10 you get wont ever cover them all.
If they wanted to go with a perk a level system then skills should be good on their own but become great and or gain new features with perks.
The core design was flawed and then most of the perks end up being lame on top of that. For magic they could have gained inspiration from 3e D&D's metamagic feats, for physical skills I would have looked towards 4e D&D and their idea of martial powers. Not outright copy mind you, just the general ideas as inspiration. As is we got a list of boring feats many of which are poorly balanced even if they have uses here and there.