The biggest problem with CTF in TF2 is that TF2's best style of play is with a front line that moves through the map, with one team advancing, taking ground, then with their engis and snipers, holding that ground; then advancing again. Dustbowl has this, Gravelpit has this, payload maps rather explicitly have this (the advancing payload is the rear of the front line); even the 5-point linear CP maps behave similarly.
With the typical TF2 CTF map, you don't get this: the area you're trying to defend is not your newly-taken ground, it's way back at the farthest point of your base. And you can't--particularly in 2fort--form a front line, and take ground, as your enemies are spawning around you, or even behind you if you're in the enemy base.
The other big problem with CTF in TF2 is that both teams have exactly the same goals: Each team is simultaneously defending and attacking, and you don't get the different dynamic on each team that attack/defend maps of any kind give.
One of my map ideas was a CTF map that would try to take the best of TF2's battle style and adapt CTF to fit. I'd planned a map with a single flag; one team's job is to defend the flag, the other's is to infiltrate the base, pick up the flag, and return it once, for a single capture; the flag would have no timeout, so that it would progress steadily through the map.