I figure after Crossfire/Blitz have been brought to as close to perfect as possible, the Uber Team will hopefully move on to new game modes, and Capture the Flag would be the safest bet. Perhaps you need the bots to lower the shields around the flag, or something similar. Oh, and instead of Capture the Flag, make it Capture the Cheese, because cheese is delicious. Remember what Mickey Cantor said.
I proposed the idea a while back that only bots can carry the flag back to your base and when the flag carrying bot dies, the other team has to retrieve it. Like a timed flag retrieval type of thing (Halo). Only problem with this is that the bots would have to be significantly stronger so they don't die so easily.