After spending hours retweaking the 3DS part of the framework, I'm now mostly confident that everything's a little more compatible.

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The framework's save now happens over about 20 or so frames, piece by piece, with a little swirly blob in the bottom right corner.
This will be the case over all systems, and I've added a bulk "speedy-last-minute-save" if you happen to quit prematurely.
As well as this, I reworked the level generator for Micro Clampett, so that it, too, takes place over several frames. It's now taking about twice as long to run, but at least it no longer stutters horribly whilst doing so.

As well as that, I had to poke around in the File-Reading commands, looking for a weird issue that would only crop up in certain circumstances, and only on the 3DS.
Again, this was one of those "Hardware only" issues, which the emulator happily skipped over, so it took a fair amount of work (tweak, compile, copy to cart, reboot 3DS, run, crash, repeat) to track down the problem.

But everything's flowing a little better, and the major bugs are all disappearing bit by bit.

Now I just need to make a game for this week..
.. And it's already Friday!!