There's nothing wrong with a kludge, aesthetics aside. Every evolving line of discovery needs it's necessarily flimsy connectors of reason. It's only when we allow our pride/ignorance/greed etc. to deny that the kludge is just a kludge: this is where mistakes are made, and thus we fail to evolve.
The fact that the universe may not boil down to 3 categories of matter is not earth-shattering. If we discover something to the contrary we must look at it plainly.
The problem with kludges is that it's only a kludge when it's a theory that is revealed to be inherently flawed. Before this realisation, it's just the best theory we have at our disposal. Just because something is revealed to be inelegant doesn't mean it wasn't serviceable, or simply the limit of our reason at the time it was presented.