>>43638799Gen 7 had a good idea going with Totems. My post isn't necessarily about villains, but about bosses. Pokemon with embiggened stats and the ability to turn the fight in their favor by calling assistance are what makes totems totemic and you could expand on the concept easily.
Pokemon is one of the only RPGs where boss characters have to be on the same tier as the player. For example, a Pokemon like Mewtwo as a boss could have higher base stats that get lowered and normalized for a tougher fight. Maybe Mewtwo has a gimmick for it's fight, like cloning one of your pokemon and using it against you. Maybe Rayquaza's gimmick is that you need to use a Pokemon capable of flight to beat it. Maybe Giratina's gimmick is that Inverse Battle rules take place while you're in battle. Maybe Groudon summons lava and inflicts damage at the end of the turn unless you're battling it with a Ground, Rock, Fire, or Steel-type, and even then you have to be wary of Groudon's own Fire and Ground-type attacks. Maybe Palkia has Gravity and Dialga has Trick Room. Maybe Arceus is immune to status conditions. Et cetera. All sorts of shit.
These are in addition to abilities, not replacements. Just ways to make the fight more difficult and interesting. This isn't even addressing the other pre-existing methods that could make a fight harder, like IVs, EVs, held items, Auras, etc.
For a story boss legendary you just have to defeat it to get it to join you and select a vacant pokeball in your inventory, like for Zekrom in BW, etc. For the optional ones, like Landorus in Gen 5 or whatever, you have to whittle it down and capture it as normal. Maybe they can adjust the capture rate for this. I don't know. I haven't played Gen 8 but maybe Raid Battles lend some ideas here. Maybe you get rated for how well you did against the boss mon and it improves the likelihood of catching a shiny or of the pokemon holding a rare item
