Making Tracking and Trapfinding solely skillbased...

[Coidzor]

Are there even any PrCs whose requirements would need to be significantly altered to account for such a change?

And what, if anything, would you give in place of such things as special abilities?

[Togath]

To replace track(as a bonus feat) and trapfinding(as a class ability) you could add either a +4 bonus to appropriate checks, or make a scaling bonus equal to 1/2 their class level + either their intelligence modifier(for search) or their wisdom modifier(for track/survival), or a bonus equal to their class level

[ffone]

To replace track(as a bonus feat) and trapfinding(as a class ability) you could add either a +4 bonus to appropriate checks, or make a scaling bonus equal to 1/2 their class level + either their intelligence modifier(for search) or their wisdom modifier(for track/survival), or a bonus equal to their class level

I wouldn't recommend adding the Int/Wis modifier as a bonus, as the underlying skills already use an ability score (i.e. adding the ability score twice feels odd).

Also this would drastically change the typical difficulty of traps (i.e. +10 or +20 at 20th level), since the party trapfinder is often already a single-classed rogue. Doubly so once the character realizes that by taking 10 they will pretty much always ace anything which was originally remotely CR-appropriate.

Maybe let the ability reduce the time the checks take, or allow taking 10 (i.e. people without Trapfinding or Track can still use all the uses of Search or Survival that are normally prohibited, but they can't take 10, or take twice as long (i.e. Track is like a Swift Tracker which everyone else lacks), or something. I'd favor the latter, since not allowing take-10s may increase the time spent rolling - like, four d20s for every 5' the four PCs walk...barf!)

[Psyren]

Pathfinder removed the Track feat, try their version of Survival. (http://www.d20pfsrd.com/skills/survival)

As for PrCs that are altered, Slayer is the biggest one I can think of, but Pathfinder fixed that too.