If someone's spamming projectiles and running, there's a chance a bomb finishes them off, which is their punishment for dragging out what's supposed to be a quick tie-breaker.
The problem with 1-stock matches is that you can have anywhere from 1-4 (soon to be 1-8) players playing at one time. Just because a competitive community exists doesn't mean this game magically became Street Fighter. Understand that this game caters to many people, and has to compensate for many people. It isn't just our game, and asking for the time to play out an entire fresh stock while people are waiting to play is selfish.
The problem with % wins is that someone can just camp and hide to win in a match with many people, or the guy that plays safe and kites all day would win, even if their KO potential is rather low (thus their design would be based on racking up % for the KO, not for a free win condition if the timer's low).
If we do 2 stock/5 minutes, unless it's two campers, there's very little odds of the game going to time in the first place, even with 5 minutes.