Did you... not train at all?
Anyway, it is likely that you will have lower level pokemon than the gym leader by that point. But let's be honest, the player has a huge advantage by being able to use any pokemon they want while the gym leader is for the most part stuck with one type or another that you can exploit. And the Elite Four are meant to be the best people around, it's only logical that they have raised their pokemon to the max and have stuff that's in the 80s. As long as we have multiple engaging sidequests (which any great fangame has many of), there shouldn't be much more grinding than canon games already have.