Skills in a class-based game...thoughts?

The traditional complaint about the thief class in earlier versions of D&D is that it adds a new class of abilities, skills, to the game. As D&D went through more editions, proficiencies were added, which are skills but they are not percentage-based like thief skills are. People have proposed alternative "skills" for thieves, but from my perspective simply changing the dice used, to say 1-2 on 1d6, is simply a different way of presenting a probability, not really a different fundamental solution.

I never liked the way skills were handled in AD&D 2e, or 1e for that matter. They took a different path with the Palladium system and fully embraced percentage-based skills and integrated them into classes. The Chaosium system, which shares a definite heritage in OD&D, integrates percentage skills but does away with classes altogether, defining what a character is by his/her collection of skills.

The only point to this is that I'm curious to get peoples' different perspectives about these ideas.

Discuss!