Don't forget that it's also possible for the flag carrier to drop the flag with F, wait a few seconds, and pick it back up to "recover it normally" all over again (or have a teammate pick it up right away).
How about...if a flag gets dropped by any means, and its last known holder was an opponent, then upon being picked up by a teammate, the timer will start: 10, 15 seconds...whatever. When that timer runs out, the carrier buff stops applying, and nothing can cause the timer to reset except an opponent picking up and losing the flag again. (Of course, setting the flag in its stand and leaving it there relieves the buff of its contingency on any timer.)
Protect mode is another wrinkle. The theme of that mode appears to be "take your flag with you to get the increased firepower you need to break through to the opponent", which would suggest that it wants the existing behavior to continue wherever GSP3 is set. Once you grab an opponent's flag, they either take you out successfully or get it back at their base 15 seconds later, which prevents the tactic of sitting on both flags with a lead, refusing to score and running down the clock while no one else gets any buff to go head-to-head with you. (Unless, that is, you can stake out a hiding spot and repeatedly drop the flags as necessary to prevent the game from registering a capture, all the while hoping the opponents don't find you and scoop up the flags themselves once you drop them.)
Also, in stock 1.4, protect causes a player to automatically pick up their own flag just by running over the stand while it's there, a behavior that SVN no longer replicates. What led to that change?
In defend, you can't pick up your own flag under any circumstances, which is the defining feature of that mode. Instead, an opponent can rush in toward the fallen flag, helped by the spawnprotect interval. If the flag resets after 15 seconds loose, and it's been 13 before a player sneaks in to grab it, then even if you put the opponent down right away, the timer goes back to the full 15 seconds, plenty of time for them to come back and repeat. With this kind of activity going on at both ends, it leads to a bunch of scoreless draws, and nothing either team can really do about it. I've suggested this before, but my idea here is to keep track of the reset timer even while a flag is being held. If it was picked up 2 seconds away from resetting, then as long as that player can hold onto it, the timer would count up at an equal rate: 3...4...5...and on to the maximum 15. If the flag carrier gets killed, the timer starts counting down again from wherever it left off, and this lets the defenders actually accomplish something, instead of uselessly gunning down an onslaught under the impossible prospect of having to keep the flag untouched for an entire 15-second window all at once. It's still harder to score there than in vanilla, no doubt, but there's a difference between "harder" and "never gonna happen".