I'm lost here... you take it from one tank and bring it to the other? The bots seem confused. They keep trying to go to spawn with the flag.
I do like the idea of a moving flag, but I feel the level needs to be longer for that to happen.
I feel like the safe room needs to be bigger. Right now it seems to be an H shaped hallway.
This is a good and creative idea, I just feel its too easy. It is very open and you can easily avoid people if not just flat out kill them, keep running and get the flag before they've even respawned. There will always be an open hallway with nothing in it that will be easy to run down.
The areas feel so big that they can't be properly covered with sentries. Spies don't feel useful because of this, and not just because of this, but because the action is so wide open and if a spy is covering 1 alternate route there is another alternate route a person could take. Snipers don't feel useful as they could. Demos don't feel useful due to lack of sentry points, but maybe its just the way I'm playing. Scouts.... pyros feel very useful. I'm gone and over everyone's head by the time they notice me. It feels more like a race than actual skill.
Perhaps this means you should seal off 1 of the 2 alternate routes at each point or tighten up the hallways of the alternate points.
You could even have 2 tanks start in the middle and go away from their spawn points instead of toward them. Then have the drop point at home base if that's possible. That way people have to go further each minute they play instead of going closer each minute they play.
After all of this is said, its still a clever idea that you should continue with.