but we can't emulate the 3DS fully right now
You do not need to be able to emulate the 3ds fully, just edit the binaries which we can do. You can even do it in hardware.
It is a very annoying hack to do though, hence why there are so very few on any systems, let alone one as relatively new to hacking as the 3ds. The 3ds actually being a half modern computing device with a kernel and processes and such might get in the way a tiny bit and yeah the option to trick it into running at a higher speed on the n3ds if it is a 3ds game would possibly also be one somewhere
I am lacking time right now so you would probably be better off hunting down a DS thread for similar questions. Generally speaking though there are three methods, assuming you do not just mean optimise the game which you do not here.
1) vblank loops. Probably the easiest to attack but gains the most fallout. Screen updates tend to be tied to vblanks and that also accounts for various pieces of game logic that might happen. You disable some of the vblank loops and have them happen all the time (or some more frequent event) instead and you probably get some garbage on the screen and some speed increases too. Traditionally this was tied to the clock speed of a device which in turn went for the screen it went on hence bad PAL conversions, different clock speeds between regions and even old dos games being crazy fast on modern machines but newer devices often have a separate timer, hence PC games working just as fine on my P4 as they do on my oced i7 if they can keep up, or indeed the same on the PSP whether it was underclocked or clocked faster.
2) animation based tweaks. If a game will wait for an animation to happen you force it towards the end state faster -- if it waits for an animation to happen over ten frames you have it happen over one. Works for 2d and 3d animations. Hopefully said animations are not a loading or calculation mask. I see pokemon in this instance is using a fairly well known 3d format and animations to match, good times. Similarly many years ago I played pokemon blue, it had a little experience sharing device. I took it off in the end because the thing made me press A a bunch of times at the end of battles, you shuffle all that into one line and you increase the speed...
2a) crank it to 11. If a game has a setting for text speed and such then it might have an option to go to, if I am allowed to mix my films, ludicrous speed -- if you are familiar with cheats then you might have an 8 bit variable. That is a whole 255 combinations but high speed might only be value 90...
3) Full blown hack. If you don't have anything nice to abuse like in 2) and 2a) you fully analyse the game code and make it happen, first step there though is to see if you can force something like 2) or 2a) to happen if there is a bounds check or upper limit put in place for whatever reason.
Of course the other option is cheat -- if you are only grinding and grinding in this case takes no skill then skip the middleman.