If you missed my steam message, I gave you some annoying general feedback on running through
Bases feel a little cramped as in it feels like you're always running through a corridor to a location. The only somewhat open area is by where the flag starts. I suggest removing a wall or two somewhere in the base to make it a little more roomy but I don't have an idea where right now. Corridors aren't bad but these seem a little longer than average.
Having to hold your own flag to cap is a bit extreme... if there's too much capping going on maybe not make the intel move so far out in center (but still move out some).
Changing CTF mechanics is good, but I think it'd be good to do it with small steps. I know one thing that did NOT work in my maps when I was porting them was a different spot to capture the flag than where the flag was. People just get confused, even if there are some signs. I'd make the capture point where the flag starts out initially.
Overall the cart moving the intel is a good idea but the other CTF changes seem unneeded. The moving intel already creates a moving target for offense and defense which seems like enough to swallow as is.