While I've got no problem with the concept of perks (I'm not in love with them either, could go either way), I felt they were implemented terribly in Oblivion. Both how you got them, and what you got. Aside from the clunky format of handing you one every 25 skill levels, I disagree with giving everyone the same things. Your skills basically define who/what your character is, at least as much as your choices and roleplay efforts. What if I want to play someone who's just a genuinely good speaker, and exists on a moral high ground? Too bad, you get all the bribery speechcraft perks anyway.
I've always disliked the "you can never fail" aspects of Oblivion, which made me all the more annoyed by most of the perks taking that even further and removing all penalties, which just made characters blur together all the more. Mastering both armor types made them identical. Weapons gave you the same bunch of power attacks, magic perks were worthless, those two covered most, and the rest mainly just removed penalties or stacked bonuses on top of what the skill already did, as if getting better at it weren't the point of raising the skill in the first place.
I'd like to see a much larger number of perks, each much more specific in its function, and have the player decide which they get. Example of how this could work: you select 2 perks for your major skills and 1 for the minor. In-game, raising skills gives you "perk points." Say I raise a skill to 40, and have 40 points. I could then go to a trainer and "buy" a perk, i.e., be taught a specific ability. Instead of getting them all, you have to choose the ones that fit your character. You could also learn them from events and actions, such as how you get the Finger of the Mountain spell. Find a rare, ancient tome and learn a unique magical perk, or as a reward for performing a task for a daedric prince. They should be different between skills, including between weapon skills, not the same pile of power attacks. It would be a more intuitive way of getting them and also allow for greater customization, instead of spurning it.
I dunno, I'll agree that the never failing is unrealistic, but I like the direction that oblivion was taking with combat in general and making 'failing' less of a luck issue and more of a skill issue. I mean, it made NO sense in morrowind how you could miss something so close to you that your practically hugging it. So i like that in oblivion if you miss, its your fault, not luck's, but I wish there were a lot more skill involved. I mean, honestly, i can't count how disappointed I was the first time I hit someone when my cursor WASN'T actually aiming close enough to his body to realistically connect.
And I'm more of a "make everything available to everyone" kinda guy, so having to choose between perks and loosing others kinda urks me, but thats another issue. I personally don't like perks at all, I would like a graduated system, where the perks are always there, but they get better slowly, as your skill level rises. Otherwise growing in skills becomes arbitrary and all about "getting to the next perk" every 25 levels. For example, jumping on water for acrobatics (pretty useless anyways, but hey) is always possible, but the timing required at low levels is so ridiculously specific that you'd just plain have to get lucky to pull it off, where as at level 100 you can just kinda repeatedly press jump across the water willy-nilly to perform the feat.
It just seems kinda unrealistic that one second your incapable of something and the next your not... thats all...