Even with the main games, I think there's a lot that could be done. For example, the fact the Gyms are still type-based is a bizarre anachronism. Back in Red and Blue it made pretty good sense because they were actually very cleverly designed to push you towards certain objectives. If you didn't go Bulbasaur/Squirtle, then the only Pokemon which had moves at early levels that weren't NVE on Brock's Pokemon was Butterfree (Confusion). Everyone else (Rattata/Pidgey/Spearow/both Nidorans/the Weedle line/Pikachu) were pretty much stuffed, so having Brock be specifically Rock type provided an incentive to spread beyond your initial line-up.
Similarly, once you reached Misty, if you hadn't already caught a Pikachu you'd have no access to Electric types because it wasn't possible to get back to Viridian until acquiring Cut. In doing so, the game forces you to thoroughly explore Route 24, where you could find Oddish/Bellsprout. Lt. Surge forces you to explore Diglett's Tunnel, because the only Ground types you can have encountered so far are Sandshrew, which doesn't learn any damaging Ground type moves, and Geodude, which doesn't until level 31, at which point you'll be long past Lt. Surge.
Pretty much all of the other gym leaders in RBY function in the same way. The types have been quite carefully selected to push you out of your comfort zone and teach you lessons. It's no co-incidence that Fire types and Erika's gym become available at approximately the same time, or Ghost types and Sabrina. However, after RBY this just stops being the case. GSC's gym leader line-up doesn't have any real gameplay reason to be the types they are, they're just the left-over types from RBY. The only purpose they serve now is making the game easier, because you just need a Pokemon of the one type that can sweep them, which there's a high chance you'll already have (as opposed to RBY, where the order the leaders were in mandated you hunt around).
This has gotten even worse over the generations, because now Pokemon have much, much wider movesets and you don't really even need to be that specific about your Pokemon choices. It used to be Pokemon would pretty much only learn moves of their own type or Normal type naturally, and anything else was by TM. Now pretty much all Pokemon have strong moveset variety which means most Pokemon can handle most situations with some careful selections, degrading the importance of gym leaders being single-typed even further. As it currently stands, single-typed gym leaders are one of the most disappointing features of Pokemon games. Particularly in Yellow, the combination of high levels and limited availability of tools made gym leaders really quite difficult. Now? Meh.
Gym leaders should become far more like Frontier Brains, in that rather than being built around a type, their team is built around executing a particular strategy.
Sorry, that was a rather focused post around a single example, but there are many more ways in which the main game content is due for some big changes too.
) is that you can even remove the cap! I hope retro costumes will be available and that it'll be possible to mix things around.
