Traps.
I like the traps rules as is. I see the classes as less RP-oriented, and more RP-neutral skill-sets. A level of rogue includes training in the disarming of more complicated and magical traps. So a PC who wants to disarm complex traps needs to take a level of Rogue. It's just that simple. Just as a PC who wants to channel positive energy needs to take a level of Cleric, even if he isn't particularly religious.
In game, a Fighter19/Rogue1 can portray himself as a pure warrior who happened to be trained in disarming traps by a fellow inmate while he locked up in prison. The level of rogue doesn't mean he's thief-like or shifty or anything.
Actually, players presuming that they know about a PC by the class-levels the PC has taken is a pet peeve of mine. I once had a Fighter/Rogue who was, in-game, a dancer/martial-artist. She would have been insulted if she were called a thief, and I was annoyed when a fellow player once referred to her as "sneaky" because she had rogue levels, even though she'd never done anything sneaky for the entire campaign.