>>56006576I personally would like to keep my OCs as distant from any instance of the "game protagonist" character, mainly because involving them in any direct manner causes more harm than good. Even replacing them entirely is somewhat of a handful, as it directly clashes with the game canon, and you basically have to work your way up everything that happens.
At best keep them around, acknowledge their feats, and possibly have their actions hold consequences. For example, if you're gonna keep the Platinum protag, the ramifications of them having caught/befriended Giratina may involve the apparition (be it purposeful or accidental) of Alpha pokemon, and possibly even Hisui era pokemon, in a modern setting. Or the SM protag's involvement with Ultra wormholes, or just about any protag's involvement with taking down the local villain team and the consequences of that.
All in all, having them coexist, even though they act in complete parallel to each other (ie their paths never cross at any point ever), is much more convenient than inserting them in the game protag role and hamfisting everything into shape.