I think the debate gets stuck between the RP people and the more casual RP/Adventure type gamer. This game excites both types so there are going to be differences of opinion.
IMO, the perks are just fine. Eventually you settle on a play style that works for you and is fun. Even if you use magic, melee and bows you can put perks into all 3 of those and stuff have a very powerful character. Think about it, do you really NEED to get deep into more than 1 magic tree if you do a lot of melee or bows? Or any other tree for that matter? If you're playing a "jack of all trades" type of characters, the perk trees will enhance all of your base abilities. Besides, if you do play that type you likely aren't going to use specialized moves that the perk trees give once you get high up anyways.
Problem is, this isn't the way the game PLAYS.
Take the companions for example, the very first quest for them is to "duel" their leader. If you attempt to use any magic on him, he just laughs and it does no damage.
So if I CHOOSE to go the path of a "mage" and finish up all the college stuff and put all my points into magic, when I get to the companion area I'm completely screwed because it REQUIRES that I play outside of magic.
The game wants you to experience all aspects and systems it has to offer through the different guilds, yet you're forced to be "stuck" with one or two via perks. Not to mention the fact that to craft good items, you need to seriously limit what you can actually spend on combat/game play perks.
This is a single player game, if there are people that are so inclined to "role play" their character...there's a simple solution.....Don't use this feature.
But stop limiting everyone that plays this as a VIDEO GAME for FUN.