I think it's great that Opeth have relatively kept the same sound throughout their career. I've never particularly noticed it before, but compared to bands like My Dying Bride, Anathema and Katatonia (three of my favourites), Opeth have maintained the standard and general feel in all their albums.
But to the point- a thing that I don't like about them? I can't really think of much, but perhaps the poor drum production in the early albums. Although I love Morningrise as much as any album, so it's possible I'm just trying to find faults in a faultless enigma.