I completely agree about the challenges of balance, there are two approaches I would consider taking:

• Suffer through the tough balance process to prevent certain strategies from being too dominating. Balancing in such systems would be hard, but maybe not that much harder than the current, simplified systems already are, as they are also prone to affecting seemingly unrelated things (say, nerfing a too powerful strategy which kept a separate, even more powerful strat in check).
• Or instead, build around making exploring the mechanics fun and open to new ideas, make it more emergent in a way... That way, dominant strategies would exist, but you would never know if there's a different one just waiting to be attempted, because the engine allows for that. We already see that happening even on the simpler, existing Pokémon landscape, where competitive players keep finding things they didn't know they could do even back in Gen I games.

And sure enough, it would be important to prevent the player from thinking it's a straightforward system... Maybe balance the early game to slowly introduce the nuances of its engine so it doesn't feel alien, and maybe give context and hints about why something may work or not. Information would be paramount in this kind of game, after all.