___ I like the idea of modding the leveling system and perks. However I would rather see it change so that when the next TES game comes out the Bethesda could earn from its experience (harvesting mod from Oblivion being a great example).
___ When trying to fix something we need to think whats best for the game experience rather than real life solution: breaking down armor and weapon (like for enchanting) to learn recipes isn't a good idea, but making it a quest to talk to someone, bring and read a book and then eventually bring one special quest armor piece to reassemble is much more fitting in therms of game logic.
___ I think that at the end of each tree the master perk shouldn't be like any other. Player would have to quest for it, but also gain it through that hard quest, as he proven that he deserves it by this quest, improved skill and others perks invested.
___ Instead of removing the importance from non-combat skill we need something better to do with them - speech and others usually comes down to possessing lots of stuff and money, which means that we could have character invest their money. If instead of grinding weapons I could buy myself a bodyguard I wouldn't be afraid to become non combat character.
___ I love the idea of character's stats (health, magica, stamina) improving though normal playing - they would just increase with the skills - if you want to try giving something to a player at the level up I suggest 3 new stat points: strength (gives additional damage to weapons), dexterity or agility (that makes character move faster) and magic power (that adds to the power of spells). I don't know how much the new stats should improve the character (should the bonus be added before or after the skill multiplication), but that's something to calculate and test out. New stats will allow to make custom character, while removing the need to decide on how much health and stamina should a mage or thief have.
___ I'm very found of the idea that
TheCastle have mentioned before about disallowing the stat to progress unless an perk is invested in them. This also helps with the problem of grinding the skills you don't use.
___ Some may complain that this way we won't be able to play as master of all, but the perks had that in mind, while the Bethesda wanted rather play it safe and do the changes to TES more slowly (e.g. you can kill off one guild - the Dark Brotherhood, the other one is the war quest line that suggest multiple play through, which suggest that in the future we can see more of such harsh possibilities for the player do choose since people didn't flip about that, and accepted such possibilities).
___ Grinding every skill to 100 is something unnecessary and not for everybody, and be honest - there's pokemon games for people that likes that in game.
___ Unaccessible skill progress suggest that a player with limited amount of perks won't be able to reach such high level as 80 with the current level number, which will also require to redesign the whole world leveling - dragon and dedrastic weapons/armor become easier to find at level 70th than 40th.
___ To better test that the beta character should have all perks available at the beginning in order to see how much he can progress he can made and how much skills unlock. This would later show when and how much perks should the player gain - on level ups or maybe through questing? What perks should be required to unlock further improvement of a skill: a number or already decided skills. In magic school the novice - adept would be a easy place to set designed blockers, but different skills with not so linear progression would suggest that the number is a better choice.
___ The number of perks invested in skill should increase the speed of training it. The player should be able to increase many skills to certain degree rather than mastering all selected ones - e.g there could be a perk that the player is interested at 70th skill level, or mastering of lock-picking isn't an necessity to keep playing.
I leave that here for discussion, since I guess that's enough to chew on

EDIT-
Athleticism skill:
It should be a combination of both athletics and acrobatics and if it would allow a player to climb - it could be just climbable walls at the beginning (building could have walls like that), but that gives additional possibility for archer characters since not every archer wants to be stealth character.
I guess that this skill should improve all moment: running, swimming, jumping and climbing. It all would be done faster and at lesser stamina cost as the skill progress but some things shouldn't be possible without the right perk. Perks itself would spread into 4 branches:
running: allows dodge moves > sprinting changes over time into dashing (after few moments of sprinting character starts running even faster) > bash move (pushing to stager opponents executed by dashing at them)
jumping: allows roll move > reduces damage from falling > allows to battle while jumping
swimming: allows to swim in armor (going into deep water unless your argonian could cause death) > allows to fight while swimming > improves fighting while swimming (damage and speed would be reduced under water, so this perk would lessen it - it could be branched to close range weapons and projectiles, and I don't know about magic)
climbing: allows to use ropes > allows to use climbable walls > allows to battle while climbing
Of course like with sneak skill it's easier to improve this one while using something more than running and jumping (that would be a chore, and protect people that aren't interested in it from leveling too fast - everybody runs but if you fast travel you still can level it normally without big disadvantage) - cause sneak improve the best with sneak attacks, so athleticism would improve best while fighting under water or climbing.
Master perk could involve an quest which would add to the walking,running,climbing and swimming speed and jumping height. Only one branch would be required in order to reach the Master perk after reaching 100 in this skill.