As far as I can tell, aliens would have a very large advantage over humans in CTF (being able to hide much better, walk on walls to get to better places, much faster, much quieter, regenerative HP, etc) so in order to make it more balanced you would need to give humans something or do something to make it more fair. Humans have always had the advantage in that their bases can withstand assults better than the aliens can, but I assume you won't want bases in CTF, anymore than telenodes, arm, medi, egg, and maybe booster, unless you just set the area around both flags to nobuild area, because otherwise camping will make the games horrible.