I would love to do some CTF in this game.
Few quick thoughts:
While you have the flag, all travel powers suppressed along with given travel powers/buffs like SB and IR. (This would also solve the problem of having to worry about SB buffing -speed resists.) I think the exceptions I would make for this would possibly be sprint and maybe swift/hurdle.
I don't think it's a good idea to disable powers on the flag carrier when he picks up the flag. Can't really recall any games that do this, although I'm sure there are some. Seems like it takes some of the fun out of the game not being able to defend yourself.
I do think there may need to be a debuff or something of the like on the flag runner against defense but this would have to be watched closely as you don't want to make it too easy to kill the flag runner but you want to make it so they NEED support getting the flag back to base.
With these changes, I'd be a bit concerned with the target aoe powers like ice slick that slow. Once you get 1 or 2 of these down, the runner isn't going anywhere and I can see ice or earth trollers camping their own flags to keep a patch on the ground letting no one get out of the area. I suppose the counter to this is to kill the troller. It may not be an issue but would need some testing.
Phase shift and stealth powers would either need to be disabled or would auto drop the flag once activated.
Something like this would make not just stone tanks, but most tanks more viable for pvp, maybe even more scrapper builds.