The vast majority of creatures in the game are evil, and thus are affected by holy. The only ones that aren't (that I can think of off the top of my head) are Animals, Vermin, Elementals, Oozes, Constructs and some Aurum members.
Pretty much all Orcs, Goblinoids, Reptilians, Giants, Undead, Elves (Drow), Dwarves (Duergar, and with the exception the aforementioned Aurum Members), Aberrations, Dragons, Monstrous Humanoids, and Magical Beasts (though a few of these might be neutral too) are evil.
So, in essence, Holy affects half, if not more, of the things in the game, whereas a Bane weapon will only affect a small portion of them.
I dislike them, partly for the very reasons you give and partly because I disagree with your reasons.
1. "Prestige Classes" should be choices as important as taking a level in anything else. You shouldn't be able to just switch from one to another on a whim. The enhancement version of the system essentially lets you be an assassin one day and a thief-acrobat the next. This is out of keeping with the way the prestige class system is designed to work.
2. You can mix-and-match less. In the real prestige class system you can take however many levels of however many prestige classes you want. If you want to be half one thing and half another you can do that with all the same benefits and penalties that come with regular multiclassing. The enhancement system prevents you from doing this by limiting you to one "prestige class" at a time.
3. Regardless, prestige classes are a large part of D&D 3.5 and ought to be given the development time they deserve. Enhancements, on the other hand, are something Turbine made up out of whole cloth with more than their fair share of development time (including an entire update devoted to fixing them) and have actually done much of what you worry the prestige system would do (create drastic imbalances between various races and classes).