First of all I want to apologize to Prime for putting this subforum up and me not posting in it for a good while. Job hunting is cutting into my development time, so I haven't been making much progress.
Second, I've reconciled my first draft of condensed skills into the following list:
Acrobatics [Dex/Con, Balance+Tumble]
Antagonize [Str/Cha, Bluff+Intimidate]
Athletics* [Str, Climb+Jump+Swim]
Control Shape [Con/Wis, unchanged]
Craft [Dex/Int, Craft+Disguise]
Focus [Con/Wis, Autohypnosis+Concentration]
Inspect* [Wis, Appraise+Search+Sense Motive]
Legerdemain [Dex/Int, Disable Device+Open Lock+Sleight of Hand+Use Rope]
Lore [Int/Wis, Knowledges+Martial Lore]
Manipulate Device* [Cha, Use Magic Device+Use Psionic Device]
Mysticism [Int/Cha, Psicraft+Spellcraft]
Perception [Int/Wis, Spot+Listen]
Perform [Dex/Cha, unchanged]
Politics [Wis/Cha, Diplomacy+Gather Information]
Praxis [Int/Cha, Decipher Script+Forgery+Speak Language]
Profession [Int/Wis, unchanged]
Stealth* [Dex, Hide+Escape Artist+Move Silently]
Survival [Con/Wis, Heal+Survival]
Taming [Str/Cha, Handle Animal+Ride]
Truespeech* [Int, unchanged]
*These skills are keyed to one ability score to make them feel more exclusive. I couldn't think of a skill for Con alone.
That list is the basic skill list most characters will have. I haven't decided what to do with the more esoteric skills (Iaijutsu Focus and Lucid Dreaming), possibly going to fold Iaijutsu into Perform (Weapon Drill) to give mundanes access to it though I'm not sure.
Now for the biggest change: Skill Tricks. I wanted to expand upon CS' original design, but make it closer to Skyrim's perk system (only less bonuses and more useful abilities). To this end I've brainstormed nearly 100 new tricks (more than that, seeing as I wanted to turn some feats into skill tricks outright). However, I wanted skill tricks to be something of a balancing point between classes: Some get more skill tricks, some get less. In example, the Factotum would get a total of 25 or so skill tricks over his entire career, whereas the Rogue would get a massive 30 or more. Each trick would provide it's player with a new use of that skill (although not all uses of skills are going to become skill tricks).
This was going to be a major point too. Fighters, Barbarians, Rogues, and Scouts (the 4 mundane classes) would have a plethora of skill tricks in order to pull them away from the whole One Trick Pony problem, and several skill tricks would address major issues the noncasters have (Item Creation feats are now Craft Skill Tricks, and there will be a way for the mundanes to craft magic items without relying on a spellcaster).
Regarding Crafting, I was also going to cannibalize the Artificer's Infusions and other abilities in order to make Crafting more useful. Not quite sure how though.