they only work using specific set of plugins, meaning that as better plugins or better emus (such as CEN64, the cycle accurate emu) are released, then the translation is rendered useless.
No, that has no effect on the usefulness of the translation.. a newer emulator doesn't magically create translations. If you mean unusable, still no, as the older version can be used.
I always want to make changes that I simply can't because I don't know or work with assembly.
If the modifications are simple enough, you can just try to do them at the assembly level, after reading a bit about the system in question.
Instead of trying to slip in changes and alterations to the code that the game runs, what if we pulled the code out of the game and ran it as its own program?
The game doesn't run the code, the game is the code. (well, code, and also data that the code uses, such as art, levels and stat-type values)
Would it be possible to extract the game's code (or certain portions of the code) as an assembly program and have it be run inside of another program?
The code is right there in the game image, so I can't think of any other kind of (simple) extraction than what emulators already do - they run the game.
Then the master program could add to the game's functionality by writing its own functions that run in tandem with the extracted code.
The way I interpret this is that the emulator could change the game state when certain conditions trigger. The benefit would be that you don't have to insert the modified code into the game. Still, you would have to define somehow the conditions.. how much of that can be done without the usual assembly knowledge? And the changes you make to the game state should not propagate uncontrollably into the game.. if it only changes emulator output, that would be simpler. But are there that interesting output-only changes?
Then within the extracted assembly program, we find a point where the monster dies and calls the death effect. Then make a slight modification to that original code so that it instead calls a flag. The master program sees this flag called, and then executes its own custom function and draws out is own death effect, potentially even one that exceeds the capacity of SNES.
So, you'd have to know the death effect condition at assembly level. There is probably no need to modify the game to "call a flag" (whatever that would precisely mean), as it is enough to have the condition listed in the emulator end. You'd still have to change that effect properly, and know how to do so.