I understand wanting to be able to micro-manage; I play The Sims 3 and its expansions, which are the ultimate RPG* (dungeons, party interaction, moral choices, the works!), as well as various Tycoon games, and Oblivion/FO3. I don't mind customization, but I like it when it's very apparent. Yes, I am good with numbers, and can understand that STR+1 means I'll have +X damage per swing, and with the mace versus the dagger I can - and so on. But I don't want to.
Having a perk every level, and more levels that mean more perks more often (more more more), in my opinion, gives a very visible way of replacing stats but making it more fun and streamlined, while still being meaningful. In a game like DA2, you throw a few points into that class's main stats every level. You're actually not helping at all if you put points into, say, Cunning to increase a Warrior's Defense. Rogues get the most out of Defense per point of Cunning and Defense and aksdnflksadnf (at least, in my experience. I believe that there's scaling involved).
Why not just have Acrobatics Training: +10% chance to evade physical attacks, and +1 meter jump height? Maybe even have ranks, so you could buy it up to three times. (I am personally against that method if perks are the entirety of character-building, because surely the creators can think of cool ways to build from the basis.)
Back to The Sims 3: In TS1/2, you made a character by plopping a limited amount of points down into axes, Neat/Messy, Shy/Outgoing, etc. Because of this, there were really only, like, twenty or less sim archetypes. In TS3, they replaced that with Traits. Computer Whiz? Can hack databases for money and loves spending time at computers. Snob? Acts haughty around other sims, but gets a nice mood boost from primping at a mirror and is flattered whenever they are praised by another sim. There are over seventy traits at this point, and an adult sim has up to five. It's a much more interesting system than point-buy, that's for sure, and allows for more complex, interesting and easy-to-understand sims.
TS3 also has actual perks you buy with your XP, er, Lifetime Happiness points, earned by completing quests, er, Promises that come from Wishes, or buy keeping positive buffs, er, Moodlets applied. That said, I really hope that Skyrim doesn't need the "Steel Bladder" perk.
*Okay, it's not, but I like saying it. Also, TS3 is not really a good game, but it is. Bleh.