I guess it would be a pretty simple fix; they could just disable the ability of the team to pick up flags that are already in the scoring zone, like a Blue player can't pick up the blue flag on CTF. It's kind of weird that this never occurred to them, though.

For the skullamanjaro/sprint issue, they should make the 10th skull act as an oddball and replace your weapon, except without the reduced foot speed. If you use an armor ability, you drop the 10th skull.