Here are a few of my favorite ideas that didn't quite make it in to CTF.
Illusions/Hallucination - This could let someone toss a projectile at a group of enemies and cause them to see dozens of random sparkles and images (including flags and flag markers) for about 10 seconds. You would usually use it before moving in for a big attack to confuse the enemy.
I was really excited about this idea but never had the time to implement it. I also couldn't think of a class where it fit. Spy was the obvious choice, but they were already the most fully featured class: they didn't need more toys.
Speed Boost - It became clear in testing that speed was a huge asset. If you could outrun your opponent you could usually survive. That is why the flag decreases speed when carried. All too often once a flag was grabbed it was as good as captured. Slowing down the holder encouraged more fighting. It is also why the paladin saw a speed decrease. He used to be very fast so he could stay with groups and heal, but it became clear right away that speed and troilus was a nearly invincible combination.
It came closest to being given to the Pusher. Allowing them to spend spirit to move faster, push further, and not suffer any "push back" from their push. But it never quite got there.
False flags - I thought it would be fun for spies to be able to set false flags on the ground, or carry a false flag. It would appear on the radar just like it was the enemies flag, causing people to chase you while a teammate snags the real flag. I also considered adding an "information" class that had all these information related abilities, including hallucinations.
Team beacons - I considered letting scouts set down a beacon that would direct all players on their team to that location.
I also thought about letting all players toggle an ability that shows where everyone else on their team is currently located relative to yourself: much like the flag markers work. Bonus for paladins: Color coded indicators to check on health. Overpowered bonus for spies: When disguised, you see the enemy instead of your own team. (That would never happen.)
Obviously if you are a disguised spy (uncloaked) this ability would show you as being on the other team, so it couldn't be used to sniff out spies, except that someone might be suspicious when a marker disappears or suddenly appears!
None of this got in because the markers get in the way of flag tracking, we'd need a more obvious flag marker before we could use these abilities well in ctf. But they work really well for the new game mode. Although they're less needed in such a compact space.