There are lots of good ideas in this thread, and (I hate to say it) lots of really bad ones. I'll try to be brief, since there's a lot here, but I wanted to add my two cents.
I heartily agree that Armsman/Barbarian/etc are terribly implemented, because they are so extreme. A maximum of +100% damage means that the game becomes extremely polarized -- either you take the perks and win with no challenge, or you don't take the perks and lose constantly. Perks shouldn't have such an extreme effect in any circumstance.
I also agree with a lot of your core principles such as perks should not replace skills, etc. Lockpicking is an especially horrible offender in this regard (the final perk is essentially, "your lockpicking skill doesn't matter anymore!")
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I have to vehemently disagree regarding Smithing. Adding animation times and/or failure chance adds nothing to the game, and does not make it more fun in any way. Instead, leveling Smithing should depend on the value of the components you use, so that creating Iron Daggers is less important than practicing with, say, Orcish Swords.
Also, not all items should be available for smithing at the beginning of the game. This is overwhelming to newcomers and is poor design to frontload all the information. It creates a much more satisfying sense of progression to unlock new options. The quest/recipe idea is a fairly good one.
I agree that the Smthing perks are lame and could use better subsitutes. I like the Knight Tekton's ideas most so far.
I've been thinking about how they can balance the skills so the crafting skills don't level you too fast.
Have two tiers of skills
Tier 1 Combat (Archery, 1h, 2h, light armor, heavy armor, alteration, conjuration, destruction, illusion, restoration, block and sneak)
and
Tier 2 Non-Combat (Lock Picking, Pick Pocket, Alchemy, Speech, Smithing)
In vanilla Skyrim, this would be quite broken. Smithing is as powerful as any combat skill, if not more so. You can more than double your damage potential by investing a few perks into Smthing. Similarly, Pickpocket, Alchemy, and Speech all directly or indirectly affect character power. Being able to create better potions, being able to buy better items, and being able to steal enemy weapons before combat are all direct buffs to combat prowess. Lockpicking, not so much, because it's a useless skill

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Regarding Speech, I'd like to suggest tying Speech to the character's ability to use Shouts. I've already created a mod to implement it, and it works quite well.
http://www.skyrimnexus.com/downloads/file.php?id=2318
It lets you raise Speech in a less boring/necessary way, and also gives Speech a more versatile use without being overpowered.