I have a great idea for this mode. It changes almost everything but keeps the central concept of a Balloon Race.
Here are the main changes, I'll give an explanation of how it can work afterward.
You can't beam to the ships or spawn on them.
The Ships can be sunk if you don't protect them, and they respawn.
The CP can be recaptured.
Can take control of the enemy vessel?
After capturing the first CP with the boat, the team has to try and make it back to complete a bombing run on the enemy base.
In this way, and with some balancing, both teams can always be in with a chance of winning, and their will always be exciting objectives to attend to. Destroying the enemy ship or just boarding it. Catching up with your own ship, which is now feasible because the ship sails through a winding canyon which has onfoot shortcuts, and since ships can sink engineers will have enough time to make on their side of the river since.
Here's a link to it in more detail if you don't undertand:
http://betterballoonrace.blogspot.com/