I have been actually digging into it with ghidra and it is filled with spaghetti code. But the main reason it lags is that it runs the fully software sound engine at stupid high settings (despite the music being terrible). It uses 12 channels and 21 KHz. Pokémon uses 5 channels and 13 KHz.

That's really interesting. I thought the GBA only supported four audio channels. Why was the music channel set so high?