Here is the official skill list of a jim pinto D&D game. And of course every class's skill selection would also change. Effectively everyone would become a 3+Int (except rogue which becomes 6+Int). And their choices would change too (so fighters and sorcerers can do stuff).
Athletics (replaces Balance, Climb, Escape Artist, Jump, Swim, Tumble)
Craft (replaces Craft, Profession)
Disable Device (replaces Disable Device, Open Locks)
Knowledge (replaces all knowledge)
Notice (replaces Listen, Spot, Search -- allows for Scent)
Religion (includes understanding and performing rites and rituals)
Ride (replaces Ride and Handle Animal)
Social (replaces Appraise, Diplomacy, Gather Information, Intimidate, Perform, Sense Motive)
Stealth (replaces Hide, Move Silently, Sleight of Hand)
Subterfuge (replaces Bluff, Decipher Script, Disguise, Forgery)
Survival (replaces Heal, Survival, Use Rope)
Theory (includes all non-ephemeral Knowledge; replaces Spellcraft, Use Magic Device)
I haven't considered yet what is MISSING from the game. Essentially, skills are a patch for the rigid class system anyway. But, to streamline the game and reduce paperwork, this is my list. And I think you'll find it does NOT break or change the game you are playing.
Oh. And synergy bonuses are gone. Feats only give a +3 to one skill. That's it. "Keep it simple, stupid" as the saying goes
Theory could also be used to decipher scripts and runes, I supposed. Depends on your style of play.