Ok... At work now, so I can comment further on your ideas.
I agree that the skill-aura powers are kinda stupid. I just don't like your choice of boosting personal defenses instead. Perhaps change them into another, more useful aura or give them an encounter / daily power.
I agree. +4 would be too much. Perhaps remove the personal restriction and make it Close burst 20 - Target: You or an ally in the burst. That would play a little more on the leader role. Your prayer infuses you or your companion with divine guidance.
Wizard
Implements can be stolen or lost, but I agree this has no combat rules relevance. Are familiars always there or more like "now here - now gone"?
But since the casting effect of the familiar can only be used once per encounter, it looks balanced.
Spell book: First part is basically fluff (I assume that the rules state that you can't memorize spells without a spellbook, can't check at work).
Retraining and changing spells at level up: I think that they should use the same rules. So when you can swap a power at level up, you swap only one.
Power changes
Cleric - No idea, no PHB at work.

Fighter - I thought the idea of the at-will was to trade +Dam for +toHit
Ranger
Careful Attack - Good
Twin Strike - Not necessary, either nerf TS or buff CA
Wizard - Looks good
Feats
Bolt - Nice!
Essence - Looks cool
Divinity - Also cool
Knife-Fighter - Useful, no prereqs?
LSA - No more TPK through fireball. Cool feat, but maybe Paragon tier?
Roll with the Blow: This should be formatted as an encounter power.
Tap the Power: Don't know how useful that is.
Two-Handed Swing: No idea if this is balanced or not.
Warlock Implements: Really nice!
Weapon Finesse: Hm, boost to OA. Rather small benefit in comparision to Knife-Fighter for instance.
Wild Empathy: Interesting feat, with more non-combat applications than combat applications. I like it.
Multiclassing
Ranger - Errata has already confirmed that
Advanced Training: You gain 3 feats for the price of one? That sounds really unbalanced. Ranger TWF bonus is better than all the other.
Rules
Self-Stabilizing: Sounds fair.
Minions: I don't like this, but this is a personal preference.
Quarterstaff: Seems fair if you like the style.
No comment on the skill challenge changes because I had no time to analyze the original system as much as I would like yet.