Look, as someone who actually attended plenty of 3 stock 8 minute Brawl tournaments where timeouts were not even close to rare, I never once saw a tournament run late because of the ruleset. Smash 4 on average is a much faster game than Brawl, but it doesn't matter because 3 stock 8 minute doesn't make tournaments run late. Allegedly "slow" games don't make tournaments run late. Customs certainly don't make tournaments run late. Bad TOing is the sole and exclusive reason any tournament has ever run late; it's always that guy who isn't there and for whatever reason isn't DQ'd right away or the guy who is allowed to wait forever to play his loser's round 1 match and destroys the entire bracket (often this comes in the form of bias in which he's permitted to play really far ahead in another game at a multi-game event when he should always be pushed to whatever game he's holding up the most). For tournaments not run very sloppily, most of the time losses are still things like finding people or waiting for multi-game conflicts or dealing with the fact that, once again, the PM community brought ridiculously few set-ups; the actual gameplay is just not that big of a deal to the time compared to the factors that really matter as long as you keep things sane (smash 64 with no timer definitely will kill you; I've seen it a few times). If anyone has any actual evidence that tournament rules have a significant effect on tournament time compared to TOing efficiency, I'd be fascinated to see it.
3 stock is generally a better format as it makes single mistakes not instant game losses (your odds of coming back from a full stock mistake in 2 stock are nearly zero, very realistic in 3 stock), it makes long term reads more of a thing, it has less variance, and it actually encourages more diverse pacing of matches as it's just a basic fact of how people play that everyone plays way more slowly and carefully on last stock so making that half the game instead of a third of it has a pretty big effect on the pace of play. It's also just a better value for players; this thing we do these days where you have bracket pools means that the worst player at your tournament will only play two sets before elimination, and that player is likely 2-0d in both which means he only has eight stocks for his time and money. Giving him 12 is giving that worst player a 50% better value for attending your tournament while certainly not making the tournament take anywhere near 50% longer. That increases the odds he'll come back next time, and that makes your scene better. I don't think 2 stock ruins the game or anything and most of the time it produces similar outcomes to 3 stock, but it sure seems to have almost no real advantages so I'm continually mystified at why it sees so much support.