I think it's important to try to boil down the chief flaws / complaints about the system before embarking on anything.

From my perspective, what seems to be a bit off (and this extends beyond a perks discussion), is that the player character, at level 1, has a very vast body of general knowledge about a lot of skills. At level 1, the player can, with some degree of proficiency: pick a lock, competitively sword/knife/axe/mace fight, shoot a bow, strap on any kind of armor, stalk in the shadows, use a shield, mix herbs, forge a blade, and cast a rainbow sorbet of different kinds of magicka. The only skill where I have witnessed that abject failure is possible with no take-backs (at least without save scumming), is Speech.

I gather that the Standing Stones / Perk system was designed to be the way that you define your character in terms of a "class" in an inherently classless system. That's fine. The problem is that the player is already so good with so many things that it doesn't ever really feel, from the outset, that I've made a sacrifice or an important decision. I never get to say, "Ok, I'm going to be really great with archery, but be really terrible with a shield." It makes the game more approachable, but it doesn't do anything for players like me who want to make decisions, and have those decisions reenforced through gameplay.

Any "mage" character, at any level, can pick up a shield and act like they know what they're doing. The enemy won't knock it out of your hand, and you can't drop your sword or swing slowly or miss. The lockpicking system never says, "Sorry, you are completely unskilled at this, you will /never/ be able to open this lock. That's your decision, live with it." Casting a spell never fails; you just need enough magicka.

The system is too infrequently willing to say, "You must be this tall to ride." Any perk / Standing Stone / class overhaul system that brings back Interesting Decisions is what I'd like to see. I'd like to think that my character's background and life lessons have shaped him in one direction or another at the expense of certain skills. That's the whole point of a class system and something I really miss. The decisions in the perk system feel less important because I know, in the back of my head, that if I level up enough times, anything is attainable. It's less "Have this, not that", and more "have this, and have that later".

A lot of us loved what we had in Oblivion. Now we have this capped level of 81 and you are not able to level up anymore.