In my campaigns I've added a new use for Appraise: you can evaluate the general quality of an object. For example, you can tell whether a bridge will stand your weight, whether a rusty sword is still usable, or whether your shoes match your hat. Consider including this use in the manual.
If you're going to transfer uses of Spellcraft to Knowledge (arcana), I propose deleting Spellcraft altogether and using only one skill instead. Also, Concentration deserves to remain. It has many other uses besides spellcasting. For example, if you are busy trying to decipher a rune inscription on a door while your allies dispatch the zombies around you and the castle rumbles to pieces, you'll need a bit of extra effort.
At first I cried over Perception, but you've done a very good job of defining its uses. For that I'll forgive you the Stealth thing.
I love Linguistics! Consider including the Read Lips task within this skill, instead of within Perception.
What am I going to measure the quality of my knots with now?
Consider adding the 4E Endurance skill (blasphemous! yes, I admit it, but you've already got Acrobatics, Perception and Stealth). Endurance is a Con-based skill that covers several tasks that had been ambiguous before (but please don't absorbe Survival into it; they're different things).
Please, please, please, please expand the synergies. I love synergies! Once I had a cleric with ranks in Craft (calligraphy) and Profession (scribe), and it was frustrating not to have a bonus on Forgery checks.
