Is that a question or a statement?
Because thats exactly what made it great. Sure it could be toned down a bit, and make more perks selected when you start the game. Or maybe you have perks are only selected when you create your character. But anything that can make roleplaying as someone/something easier and actually matter in the game world sound great too me.
More of a statement. Take a FO3 perk like "Pyromaniac". It should be inherently obvious that the effects are much more "godly ability" than "character differentiation". It doesn't affect how you interact with NPCs, only how efficiently you kill them. In fact, of the level 12 perks, only "Cannibal" impacts interaction in any meaningful way, and that's after you kill them...
Same story for level 10 (one perk that carries any role-play benefits: Night Person) and 14 has none that aren't primarily combat or money-making perks.
That's my objection: we don't need those 90% of perks in TES.
Now, if you would like to offer TES-specific perks and cut them to every 5 levels and one to three initial choices, and have the ones with the best benefits include a cost? We can talk.
Say... "Lucky Bastard: Luck +10, Personality -10", "Morrowind Stylish: +10 points to personality when wearing a Colovian fur helm", or "Touch of Sheogorath: opens various absurd and crazy conversation avenues", these could be TES perks. Because they don't give you the means to become ridiculously powerful just by perk optimization, but you can have a heck of a lot of fun deciding what quirks and uniquenesses you wish to have.
Edit to add: Ragnalin, when I talk about excessive, that's probably because I'm thinking more "Formula One-grade" than "show that wind will eventually cause waves" grade. Which is what it'd take to really do it right to a lake vacationer