Should the rules change on game versions? As of now, any runs submitted before recent-ish updates don't have the Start-Go bs at the beginning of each level and I don't think its possible to play on older versions.

Also, should there be rules on frame limiting? It can give some large boosts.

Yes. Only if there is changes that effect the level like maps added or skips being removed.. Stuff that hinder the run. And if you mean the skip in level 2 on Midori then No I think it should be allowed.