Back then, I loved the idea of Pokemon working with Final Fantasy - certain classes having certain Pokemon, and you and your sole signature Pokemon teaming up with others and their sole signature Pokemon. You and your Pokemon also fighting side-by-side together. This can also fit with Dynasty Warriors/Warriors Orochi/Samurai Warriors (I know Pokemon Conquest crossed over with Nobunaga's Conquest so it can happen).
Nowadays, I do like the idea of Pokemon with Honkai: Star Rail (namely, because of the fun space train aspect travelling to other places) but I'm not sure how that'll work. I can see how certain Pokemon could fit in it like some of the legendaries being signatures of the Aeons, or something similar to Pokemon Masters Ex, I suppose. Same with Ash Echoes, although that'd be trickier since that is about different dimensions coming into one world (some characters even having different versions of themselves canonically showing up).