Plants/Steampunk and Ghost: Plants and Steampunk have ways to draw additional cards every single turn, but the Ghost deck is trying to discard all of its cards, and is often most powerful with an empty hand. (The Wizards get a pass here; they draw cards on demand rather than every single turn.)
Wizards and Robots: the Robot deck is light on action cards, and the Wizard deck has too many ways to allow you to play extra actions (which you won't be able to take advantage of).
Bears/Pirates/Aliens: Bear and Pirate have a lot of move-minion cards, and Alien has a lot of return-minion-to-hand cards; you're only going to find it useful to move/evict minions so many times during a game. They can still work well together, but you're more likely to have several extra move-minion cards that you can't think of a use for.
Of course, if your deck is too powerful, then your opponents are more likely to team up against you; a weak deck will keep more heat off of you. The game is powered by Rule of Cool (warning: TV Tropes) anyway, so don't sweat it too much. (Robot Bears vs. Ninja Plants!) It's much more fun to pick your deck-halves randomly than to dither over which decks to pick together.