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In particular this relates to EVs, IVs, and Natures.
The main problem with this current RNG system is that it's far easier to just inject/PKHeX your mons into the game with the optimal spreads, and desired IVs, and Natures. Than it is to breed for potentially hours on 1 mon, that it could be easy to fuck up the spread.
Unless you live in Japan where that shit is illegal. But then again the kids over there do it anyways...
A simple fix would be to give every pokemon:
>31 IVs across the board, and the IVs can be lowered by the player if they wish.
>EVs should be implemented like the showdown EV slider system.
>Natures should also occur more likely in the wild, depending if the leading pokemon in the front has the same nature, and if the mons that are being bred have the nature in question.
The battle system doesn't need to be significantly changed itself. It's already a really complicated battle system with a lot of factors even for a JRPG. Most importantly it all works in a PvP format surprisingly. Rather it should be constantly expanded with new concepts, or new elements such as new types, different types of status, or terrains, etc etc.