Matt Haughey, of MetaFilter fame, uses Movable Type in all sorts of interesting ways. Clearly, I'm also a big MT fan, but Haughey misses another significant limitation of the system: the user model is a little too primitive. For example, I've banged my head against per user information for extensions. Not fun, but doable. This strikes me as something that Six Apart should bake in in a cleaner fashion.
And another thing, can the operation of the template system be described as anything but opaque. The documentation provides surface sense for simple things, but multiple templates of different types can be treacherous.
Memo to self: kwit yer bitchin.