Frame buffer effects are the bane of HLE video plugins, but LLEs like Cen64 don't have transfer pack support yet. The GB emulator uses its own microcode too so only an LLE can run it right now, but without a way of providing it a cart that doesn't quite work. Did find a way to fake having a pak plugged in Nemu64, the only emu with a proper debugger built in.
Hadn't looked at the later titles much, but pretty much all their code is uncompressed. The only thing you have to watch out for are blocks of data outside the runtime that's always loaded. They use a special "offsetting" format so they can be loaded anywhere in memory. The offsets in the file are turned into proper pointers using a table. There are different kinds of entries for the high and low parts of pointers, standalone pointers, and jumps. So, when changing code you just have to make sure to correct any offsets that may have moved or add entries for anything new that needs them.
The sound format in all but the earliest game is a version of MusyX, later used on GC. There's a different kind that is run by RSP code, but this slightly different version isn't supported yet in SubDrag's N64SoundTools. (sorry, can't post links yet)
As for the Pokémon, they're all compressed. Their models and textures aren't really that different from anything else N64, but the problem here is the animation code is very, very specific to each one. As such, they expect the model parts to be divided a very particular way and not doing exactly what they want is usually fatal. Animations are stored separately so they could replace them easier.
Moves are basically models as well with their own animation code and ASM directly tied to them. They're really more of an event. There's a timed list that triggers calculating the damage/effects/etc. for the move, triggers different steps of the animations at the correct times, and displays the effects and so forth at the proper times. Still a bit iffy on the format specifics though.
The code is very clean though. It's not a particularly hard game to hack. If there's something specific I can at least point you in the right direction.