I was thinking on something like "until you get Mewtwo".

I don't know if I fully understand you question, but we usually time our runs using Livesplit. It even has a nice autosplitter feature that does "all the work" in starting and ending the timer according to the rules. You must use 32bit snes9x to use that feature. Well, it might be a problem to time individual levels automatically, but it may also be possible. Some people seem to do that, I didn't look into that carefully since I only did 11 exit runs.