I'm fairly certain that it isn't actually emulated, which is likely the "issue".
Something like save states is stupidly easy to implement in an emulator, it's so easy, even Nintendo does it, and they don't do things like filters and other such niceties associated with emulation. No, quite likely, if you remember the DS had perfect GBA compatibility -- which insinuates that the processor was ISA compatible with the GBA's. Fast forward to the 3DS, which is ISA compatible with the DS, and suddenly that in turn means compatibility with the GBA. In short, the games aren't being emulated -- they are being run natively. Which means that most of the fancy doo dahs with emulation -- speed ups, restore points, and the like, aren't game. You can't add features to native code, which is why native res mode has no GBA background thingy, there are no savestates, no sleep mode (GBA games didn't have it on DS either, if you recall), and the bottom screen literally just has a HEY GUYS THIS DOESN'T DO ALL THAT FANCY SHIT screen.
It's entirely likely that the bottom screen itself is being run on either another thread, or somehow the GPU is being ganked into doing it. If all it does is run "Warning screen" message and home button functionality (which would just be triggering soft reset on the system), then this entirely makes sense. There is no "Virtual" Console, only a "Virtual" cartridge.
So I don't think it's that their emulator is up to stuff, I think it's that natively running the code and losing the goodies for compatibility is something Nintendo thinks would confuse the average user. They probably assume that most Ambassadors loved the GBA enough to take that hit, but if people were to explicitly spend money on it and not have those features, Nintendo would be stuck explaining this stuff to them.
TL;DR -- GBA games aren't emulated, they are run natively, so they CAN'T improve the emulator. It doesn't exist.
EDIT: This also partially explains why they took so long getting them out (till December!). They were probably TRYING to make a full speed, zero errors GBA emulator that could be run on the 3DS, but when it failed resorted to just virtual cart'ing the games and sending them out that way. I do remember reading something along the lines of them having some troubles working the emulator, and Nintendo likes their emulators to run games PERFECTLY, not mostly good.