Another option is you could play Pokemon ultra violet which is a rom hack that combines fire red and leaf green into one game which allows you to catch every Pokemon. However I agree this feature being added in would be nice.
Unfortunately, it's useless as there's no ability to save which is the reason I hadn't submitted my version of this months ago. I was waiting for libretro to fix it.
@acraigl
I don't have a great answer for you. Specifically for GLideN64 there is a source code repository I have been checking since the project lead gonetz said a new version is imminent. It actually was just published as a specific 2.0 release yesterday. Still has some regression issues like Mario64 though.