One problem I have with the progressive genre as it stands today;
For every good band, there are countless generic, samey sounding bands. I know that this is probably true for every genre, but it seems especially prevalent with prog.
The good bands use their playing ability to do interesting, creative things. Then you have bands though who can certainly play the hell out of their instruments, but have no real creativity or writing ability.
The problem with the prog stereotype is that it really does exist, and in a big way. For every Dream Theater or Porcupine Tree, you get 100 bands who all have the same guitar tone, the same keyboard patches, the same singer, and not one distinct, memorable song among them.