I think the skill system should stick around, though I do think that the list of skills could be condensed somewhat.
I think a general Notice skill (instead of seperate Search/Spot/Listen checks) may work. I could see feats being adapted to provide bonuses in certain areas (like a +4 to spot, listen, or smell something)--it'd be a conditional modifier, which would be no different than the conditional modifiers to skills as they are right now (like the dwarf's Appraise bonus on metal or stone items only, for example).
Also, a general Stealth skill (that combines Hide and Move Silently) also seems feasible, also using conditional modifiers for certain areas, as well.
I'd argue that Spellcraft and Knowledge (arcana) should be combined into one skill (and similarly, Psicraft and Knowledge [psionics]), esp. since both are Int-based skills. If you want to still have soem distinction between knowing magic traditions & knowing how magic works, then grant spellcasters only a class ability to apply their Knowledge (arcana) skill for Spellcraft-like checks (sorta similar to the rogue's trapfinding class ability, in essence)--heck, call the class ability Spellcraft; do the same for Knowledge (psionics) with psychics, as well (calling their class ability Psicraft).
In addition, why not have a general Use Odd Device skill (which could cover Use Magic Device and Use Psionic Device, as well as possibly for using any other intricate device [other than weapons])? It'd be a way for characters to "use that weird doohickey" in any event, whether it's a magic item, a psionic item, an artificer's complex device, an artifact, or even a stray piece of high-tech equipment.
Open Lock and Disable Device could be fused into one skill, Manipulate Device. However, I could see these staying seperate, esp. due to synergy bonuses from other skills (like specific Craft skills).
If you really want to, why not go with an Interact skill that takes over the functions of Bluff, Diplomacy, Gather Information, Intimidate, and maybe even Handle Animal. Once again, conditional modifiers can apply in different areas (like a druid's/ranger's Wild Empathy bonuses/abilities only applying to Interact skill checks with animals). But, I could easily see these skills staying seperate.
But, at the very least, I could go with Notice (instead of Listen, Search, & Spot), Stealth (instead of Hide & Move Silently), and Knowledge (arcana) (instead of Knowledge [arcana] & Spellcraft).