The cap-at-flag mechanic made for some really exciting and satisfying turnaround caps. I know there were a couple complaints, but I think once people get used to the idea and adapt to it in terms of strategy and awareness, it'll be a much better CTF experience than standard 2fort rules.
I'm wondering if there shouldn't be a little bit more connectivity between left and right sides of the bases. Currently the only way to cross between them is that one thin section (whether through the doors or jumping over). That might contribute to the feeling of separation. Ultimately that might be a good thing, if it's supposed to be the ninja route, but generally it felt unused.
EDIT: Regarding the middle, I think part of it is that it's a big valley running crosswise, which means anyone trying to get across is subject to soldier/demo splash spam. You have to be on one side or the other, or you're pretty much toast. On the other hand, I liked the general amount of cover I had as medic, so that's a good thing to keep.