The best use it to improve leveling system I have seen is in Mortal Online. There are no character levels. Instead they tie things like your HP and stamina to your attributes. Attributes improve every time you use an associated skill. Both your attributes and skill points have a seperate max number. There are secondary skills, somewhat like perks that enhance primary skills. These secondary skills do not count toward your cap and cannot exceed the parent skill. MO used 1000 point cap for skills allowing for 10 max skills (keep in mind they have a vastly wider pallet than Skyrim). Now, this part plays in very well with Skyrims reduction in initial permanent choices. You can set a skill to lock, minus, or improve. This allows you to slowly retrain from one skill to another. You can also more closely fine tune your character. I locked many skills aside from armor and weapons in the 70 range to increase versatility, accepting the reduction in power.
Attributes had a similar cap, lock, minus, and improve system. The number you capped at was smaller. Each race had unique stat caps that represented their strengths and weaknesses. They even had a creative system where you choose your characters parent races to do minor modifications to the stats.
I feel that this system is more of a strong middle ground for this discussion. I think it would be best modified and adapted to meet the needs of TES in a future game, but for now I will continue playing Morrowind till good mods come out for Skyrim. It's too late for the developers in my honest opinion to fix a lot of the messes that came with Skyrim. They had a lot of better options to choose from than this perk system.