Well nobody claims they are bad musicians, most would agree that they are pretty damn amazing musicians actually.
The negative comments tend to revolve around the cheesy stuff, the singer Labre (sp?) when he does the higher notes (and a lot of people dont like his voice for any notes!) and a lot of the 'techo' stuff seems very scalar.. running up and down scales. Especially the solos, petrucci does some amazing solos, but then heaps of times the keyboard and guitars are just winding up and down a scale, copying each other exactly.. i personally think it sounds like shit and is overused in their music, but it is pretty technically challenging and some people seem to like ti so thats all that matters.
They are very talented, and they excel in some areas, but as with any bands they arent perfect and some of their songwriting techniques, solowriting techniques and riffs and so on are limited. For many people these things detract from the whole band, and in some cases its the same for me as well.
But overall, yeh, great band, i love some songs, love some bits... and really hate other parts.