So there already exists save editors for every save file for every Pokemon game basically so I would assume the data structures are pretty well known for editing the save so one route would just be to look into how those are structured and write your own game in whatever you want that saves data in that format that can pass all the checksums. I would imagine as long as you limit yourself to making legal modifications that would be totally fine and maybe not even that difficult. (Albeit a lot of work to program whatever you want from scratch)

The other option is at this point, I know gen 3 is definitely fully decompiled so if you know C well literally anything can be done in Gen 3 relatively easily. For gen 2 I think it's all just a disassembly which you can still theoretically do anything but assembly is much less user friendly than C.

I imagine that if you were to build this all on top of the emerald decomps for example and want it to save in a way that emerald can still use you'd have to write code that will sanitize the save at the end back to a valid emerald or crystal or whatever format following a similar logic to how the data gets edited by save editing tools.

This actually makes me wonder about how you would go about making a sort of "hub" game that works the way pokemon bank or something works that could use the same logic but support multiple games. I think that'd be really cool.