I agree. The idea that the fighter can be proficient with every weapon ever made and get better with it every level despite possibly never having touched it his entire career (BAB), while the bard cannot be proficient in every instrument, is hogwash. Either you go with a proficiency slot system, or the fighter is allowed to be proficient with fighting tools, and the bard is allowed to be proficient with musical tools.
I've House Ruled the 3.0 Perform back in. In a game in which I play a bard, my DM house-ruled the bard to gain 4 "perform ranks" for every rank spent in Perform. So I can be maxed in 4 kinds of Perform, or mix and match the ranks however I like among many types, while still paying for 1 maxed skill. Not as nice as 3.0, but workable.