I've played around with -moviematchlength. Works really well, especially for the games that were causing problems aqua jack, kof series, etc.
I don't know if we will find one setting that works with everything, but your findings about varying the movielength per year are what I was going to suggest. Although, one other parameter should be adjusted as well -minmovielength. The reason I suggest this is -minmovielength 800 didn't work for kof96 because it has a really long section in the middle where it displays the name and has the flame/clouds at the bottom. For games above 1990, I'd say use a -minmovielength of around 2000.
There is one more idea for games like Howard was talking about TMNT or the MK series. Here are the start and stop for MK series so you can see the entire attract mode.
mk3,178,23553
mk2,60,18251
umk3,2369,22852
I'm sure you can think of a better idea, but here are two.
1. Add a -movieloop, this would require subsequent loops have to match the first. So the loop detection would keep going until a loop matches the first, but only makes a video for the one.
2. A slight modification to the except with a -moviesamples where instead of matching the loop entirely, you match every 50 samples. So loop 2 frame 0,50,100 have to match loop 1's respective frames.
The only problem with this is when I was trying kof2000, it appeared that the fight scene was generated randomly. (Howard is that your view on it)
Howard,
You were right about the odds and to accept lower odds, but I had posted too fast. Maybe I should of worded that it is possble, where I believe you were saying it isn't. Or Maybe I've been reading too many of your posts in getting the user's to learn how to fish.

In any case, I'm not sure if one bat file will ever be possible, but the odds are getting higher.