The issue I think with designing hard Boss Battles in Pokemon is that the NPC's play by the exact same battle system you do, which means the player is always at an innate advantage of being able to think on their feet or change strategies. In a typical RPG, the battle system is kind of Asymmetrical when you look over it: Bosses have several magnitudes more health than the player, they usually take larger hits (5k on a boss vs 1k on the player is a fairly standard ratio), players have free access to healing because the bosses will beat them otherwise if the fight is a straight slugfest, buffs and debuffs may be more effective on one than the other, etc.
The Totem Pokemon or stuff like Necrozma for the mainline achieve this a bit better, since they fight you 6 v 1 (plus support adds), but have much higher stats/buffs/strong-for-that-point Movepool to make them much stronger than the average team could 1v1, and then spin-offs like Mystery Dungeon go much closer to traditional RPG structure thanks to the positioning mechanics, items, and revamped abilities making room for a lot more mechanics to mess with. Heck even the Orre games can achieve this thanks to limited easy-grinding, the more rigid selection, and the Double Battle Structure having a lot more factors on the field compared to the main game's single battles.
The greatest obstacle to hard bosses in Pokemon is the rigid focus on essentially keeping the battles to the simple structure of NPC's being "players that don't think or change teams"
The Totem Pokemon or stuff like Necrozma for the mainline achieve this a bit better, since they fight you 6 v 1 (plus support adds), but have much higher stats/buffs/strong-for-that-point Movepool to make them much stronger than the average team could 1v1, and then spin-offs like Mystery Dungeon go much closer to traditional RPG structure thanks to the positioning mechanics, items, and revamped abilities making room for a lot more mechanics to mess with. Heck even the Orre games can achieve this thanks to limited easy-grinding, the more rigid selection, and the Double Battle Structure having a lot more factors on the field compared to the main game's single battles.
The greatest obstacle to hard bosses in Pokemon is the rigid focus on essentially keeping the battles to the simple structure of NPC's being "players that don't think or change teams"