Why is it bad that perk choices define your characters ability to do something well?
Lemme put it this way...
Try killing a troll with 0 perks in your weapon damage. Pretty friggin hard, isn't it? Now take the perks and try again. Oh, that was easy.
In this sense, the perks are actually LIMITING you. You could have 100 archery, 1-handed, 2-handed and destruction, but since 1-handed is the only one you got the perks for, that's the only skill you can rely on to kill an Elder Dragon without risking your neck. This is how the leveling and perk system is more of a punishment: because the damage/armor perks are practically a requirement, and every time you level up, that's another perk spent that might not make it into archery, allowing you to use bows well aswell.
New Vegas perks on the other hand? Take melee for example: Super Slam. Gain the ability to knock down enemies with melee attacks. This is a good perk. Why? Well for one, it's a reward, not a punishment, and there's no worries of some leveling system making it so that the lack of me taking a guns perk instead will make me completely incompetent with guns vs tougher enemies; this simply means I've chosen to make my melee capabilities exceptional whereas I'll remain competent with all other types. This undoubtedly improves my performance with melee weapons. More importantly? It redefines my entire play style. Perhaps before, if I turned a corner and saw six guys with hard-hitting guns, I would choose to take cover behind something and try to shoot at them one-by-one. With this perk? Now I'll rely on melee. Now I'm gonna try to juggle them all, knocking them all down and keeping them all down so I don't have to worry about taking damage. Instead of opting to shoot back from cover and hope I don't get hit, now I'm looking for a chance to get close to them before beating the crap out of them, keeping them from attacking me in the process.
My play style, thanks to this perk, has changed forever. Not in a bad way, either: I'm still perfectly capable of playing the game the same exact way I had before, but I've also unlocked a new way to play it and a new way to approach a battle.
Skyrim? What do Skyrim perks do?
With Skyrim perks, I unlock the ability to continue playing the way I've already been playing before. Again, those perks are a
requirement. If I don't take those two-handed perks, then pretty soon I'm gonna have to rely solely on my bow for damage, since that's the one I've taken perks in. And with additional damage, nothing is changing; the enemies are simply dying quicker, but the combat is all the same. Hell, New Vegas had damage perks too, but you know the difference? Well 1) the damage you gained never exceeded 20% normal damage, which wasn't a significant amount to make the weapon-type overpowered AND thanks to the way the damage formula worked, this 20% was sometimes more like 5% extra damage (Depended on the enemy) 2) the damage was applied to specific SUB-weapon types and not the skill as a whole, making the player want to choose very specific weapon types, such as revolvers or SMGs. This, again, changed the way I played the game because suddenly a formerly svcky weapon was now a VERY viable option for my character to use. However, unlike Skyrim, the damage bonus and leveling system didn't work against me. If I took a perk that made me work BEST with cowboy rifles, that didn't mean I wasn't capable of killing Deathclaws with snipers and SMGs: I was still very capable of falling back on those weapon types if neccesary, but had that 20% extra leg up with the cowboy weaponry. Skyrim on the other hand, there could be a tough opponent I want to avoid at all costs because he hits like a truck, so normally one would think "use a bow." However, without the proper perks for the bow, it just WASN'T a viable option. I'd either end up risking it with my claymore and killing the enemy in 20 seconds at the cost of two health pots, or I'd spend the next 10 minutes using my bow to peck away at his health, using 4 health pots in the process.
In short, perks should
enhance your gameplay and your playstyle, not limit it. They should unlock new abilities and possibilities for the player, not take the job of skills, which is quite boring. I personally don't know anyone who gets excited over his Guns skill reaching 38, but I know plenty of people who're excited to get a new perk. Skyrim somehow killed that excitement by practically making perks and skills one and the same.