99 is only the best if you're in theory land or want to additionally and extensively test how much endurance players have. Even without time constraints, we would not run 99 stock because that extreme endurance skill is something we're not trying to test in competitive play. You could easily achieve a statistically insignificant amount of variance between players with just 20 stocks or something. You'd probably only marginally improve on reducing variance, while introducing negative factors or skills not deemed worth testing if you get into those really high counts.
Again though, to your point we have only kept 8 minutes relatively the same, not stock counts. Modifying stock counts to match the game seems like a wiser decision than changing the timer (unless god forbid we find out that we *should* use 10 minutes for 3 or 4 stocks, bleh).
Smash 4 is in a weird sweetspot. Ideally, we'd be running this game with 3 stock and no rage + naturally buffed kill potential or approaching potential for most of the cast and everyone would be happy. I don't have anything strongly against the argument that more stocks tends to smooth out "unexpected" or varying results between players (when we're talking about reasonable stock counts), but I find it odd that people abruptly stop that train right at 3 stocks for this game. I would ideally try 2 stock 8 min if there were concerns about timeouts at 3 stock 8 min, since we had a similar sentiment occasionally in Brawl with the proposed 10 minute timer and additional rules like Air time, Ground time, etc. Otherwise, I'd entirely agree 3 stocks is better for basically everyone sans the stream monsters/spectators that might bemoan the fact it is not as fast as Melee. The game is so new though, I don't see much harm in experimenting with stock changes since it's usually way better to explore and try new smash ideas early in a game vs later. Same with customs: I'm glad people are taking the plunge now instead of waiting 1-2 years and asking for a trial.
Many events have the time and the potential to run 4 stock events (apparently we can't even run 3 stock across the US for anything at and above state/regional size, all the 2 stock 5/6 minute events do no favors towards the 2 stock format), which should no doubt be considered "better" than 3 stock events under that argument, yet no one advocates for that. It's usually a bunch of people riding that argument without any actual ideological adherence to what is being said, just to get the same format that Brawl had. I find it incredibly disingenuous and almost as bad as when the stock count debate boils down to primarily "Well I like this more", "No I like this more" , "2 stock sucks" , "3 stock is boring and too long" etc. Where no one presents ideas or reasoning that isn't strictly one-liner opinion based.
I'm not accusing you of that, but oh my lord it gets bad. You can smell that garbage from a mile away once you ask them to actually explain something in their own words. It's a wonder anything gets accomplished in Smash 4 for rules or community consensus issues when the people around this game seem so toxic and unable to communicate like decent human beings.
I'm hoping something shows up that can reconcile the desire and concern of players, tourney organizers, and viewers. There doesn't seem to be a single format that comes across perfectly, there's always 1 or 2 groups unsatisfied with what is proposed. A lot of players are rallying behind 2 stock now, but I'm not sure they understand the possible consequences by accepting 5-6 min timers as well.