Disallow players to return their flag in CTF to their base while walking over them. Instead, place a graphical timer over the flag showing the amount of time left before it automatically returns to base. Each time the flag is dropped, the timer resets.
Reasoning?
A lot of CTF maps lock up into stalemates because a single player can instantly return the flag from almost to the other teams base to their own instantly. Teams should not be penalized for almost making it to their base and failing at the last second. The team is credited for the distance covered because the other team now has to defend the flag wherever it dropped for the amount of time on the timer. A very inconvenient situation for the team who lost their flag.
Because it is harder to return flags to base, teamwork and coordination is increased to defend flags in strange places, and the amount of stalemates decrease because its easier to score. Also, the default timer on the flags should be a server variable and a level header variable so that both hosts and wadders alike can decide what the timer length should be depending on the map and the number of players in the game.
EDIT:
Another quick CTF suggestion: Allow teams to capture the flag even when their flag is in possession of an opposing player. In the current system, when both flags are being carried, there is little incentive to return to base with it, because more likely than not, the opposing team is simply camping the flag room waiting to steal it back. If flags could always be returned at any time, there would be much more incentive to simply run back to base and score, rather than hide and camp somewhere else around the map hoping that their team can simultaneously return their flag and capture before their flag is taken again.
Not to mention this would be another stalemate breaker with increased incentive to capture rather than camp.
And last one, I promise: When a player drops the flag, whether purposely or on accident, prevent the player from using their special abilities for about two or three more seconds. The reasoning is because Sonic players can toss the flag in front of them and thok, pick it up in mid-thok, then repeat. The end result is Sonic being able to essentially use their special ability while carrying the flag, while Tails and Knuckles cannot.
sb and I both abused this to great effect in CTF netgames, but I honestly don't see why Sonic should have an even greater advantage over the other two characters.