We've also seen hype and amazing fights that didn't end in time out. At 60 seconds, it's not enough time to play a match. It's enough to attempt to, but it gives some characters chances to turtle and win/lose for ridiculous reasons. Fine example is Raiden. For 16 seconds, he's turtling to charge dropkick. That's a little over 1/4th of an entire match done turtling.
If he screws up or whiffs it, there's no chance to come back from it as you'd have to waste one half the match in total turtling to get dropkick again. Athena does not have a lot of tools to be combo intensive, but she's an excellent turtle. Leona, Goro, Clark, Maxima, Vice, Mature, and a good portion of the cast benefit from being 99 seconds. In the same breath, nobody loses anything. Athena and Leona do not lose their turtle game and neither does Raiden. Not only that, but many fighting games, even MvC3 (being a game of resets, juggles, and the Phoenix) is set to 99 seconds. You can go down the list and you'll find most choose the maximum allotted time for play because it allows them to actually play the match. It just makes sense.