I'd like to say the following:
~Bases yes!
~Flags in the bases NO!
Sorry for caps on no, but due to my days playing WoW and running around in Warsong Gultch, for 25 of 25 minutes without a win, I am not a fan of capture the flag with bases.
Instead please consider the following:
~Two Bases; set apart.
~Flag in, on, or below something set between those bases.
~~A final touch would be to change the middle ground from time to time. This could be done completely; as in a new obstacle holding the flag, or done with small or large alterations to a known middle ground.