I think one of the best improvements TF2 made on TFC is to change the victory method. In TFC, CTF was nothing more than a time limit and whomever had the most caps at the end of the time (usually a half hour) won. If your team was awful you had to sit there and take a drubbing for all map_timelimit. If their team was up by 3 caps and decided to turtle, you had to bash your head in for the full time limit on a wall of D. By adding a X-caps-to-win model, they inherently eliminate turtling. Turtling was an awful problem in TFC. You can still turtle a lead in TF2, but there's way more incentive to just get another cap or two to finish the game.
The other great improvement TF2 made was to make other game modes beside CTF seriously popular... they had a few good A/D maps toward the end of TFC but TF2 really matured them. CP and A/D I think is TF at its best because your whole team works together, instead of splitting into separate O and D teams that sometimes work to cross purposes (anyone here remember 'no chasing' or 'no midfield DM'?)
Personally, I'd fix 2fort by connecting water route to lower spiral, instead of coming out near the front door. Currently its a long route for little reward. Connecting it to spiral would force it to be defended, which forces one defender away from ramp room or flag room. Imagine the underwater fights, when dragging a flag back out this way. Even this suggestion would suck for comp play though, it'd probably end up similar to the old Well where teams would stick a heavy in the pipe to lock it down all game.
2fort is simply too narrow for offense, with the tight halls and ceilings all over the place - its a dream for stickies, sgs, heavies, and soldiers to nail down. What can a scout do in such a tight space?