Is this for the game or the site?
If its for the game I say put in a "capture the flag" style game type. That would be fun.
I assuming your talking about this topic, this topic is for both the game and the site.
As for CTF, think about this. The aliens are faster then the humans, period. A dretch can easily capture a flag on a un-inhabited part of the map, but if the flag is nearer to the human's base to counter-act this speed, the humans can camp around the flag, with or without structures. If it was nearer to the aliens, the aliens would win more easily.
That is if it was one-flag CTF. for two flags on both bases, the only way to get to the flags without dying is to kill the structures, which is basically how a normal game goes, except you don't have to kill the entire base to get points. If the flags were movable or near a large amount of structures, there would be camping issues. If the flags were in the middle or near the base, the team defending the flag would have a hard time actually defending it, especially if they're structures are destroyed.
So, in other words, doing CTF would either be near-impossible or very difficult, as significant balance changes will have to be made, which will add to the difficulty of coding it. I suggest trying out domination on th Arcade mod, you can find the Arcade mod at Servers that specify on their names with "Arcade" in it. I suggest downloading TJW's/TremFusion/a third party client to download the mod quickly. This is assuming your new to this kinda stuff, if not, my apologizes. Cheers.