In previous editions, the problem was that some weapons were mechanically superior. Plus, the prices were usually set based on (someone's idea of) verisimilitude rather than on mechanical differences. There were optional (or de facto optional) rules to try to mix things up a bit, but they were seldom used.
The 3e designers made a good effort to make each weapon mechanically different & priced such that almost every weapon had something to offer. Unfortunately, there are still a few weapons that are--or at least seem to be--mechanically superior within their class. Or, perhaps, players find some of the trade-offs more attractive than the designers may have expected.
(Sometimes superior simply means you don't have to waste a feat on it. A bastard sword is mechanically superior to a long sword or two-handed sword unless you get proficiency with the other two for free.)
I think the answer (if you think this needs an answer) lies more in the other direction. More weapons should be mechanically identical with their particular shape being pure flavor. I always liked the Warhammer FRP "hand weapon".
There's also the fact that in the real world--in any time period--there's always been a handful of weapons that are the superior choice for their role & so are nearly universally choosen when available. There's nothing wrong with the game being the same way. It's just that with D&D being the melting pot that it is, the result can be kind of jarring for some of us. (Like the rapiers v. heavy armor thing mentioned previously.)