I know, its lame but I couldn't think of anything else >.<
In all seriousness though, 1ce is right. From reading the desriptions of those plugins Jord suggested, 1ce is able to use ModDamage to have a percentage of mobs spawn with an increased health, or attack damage (as far as my knowledge of the plugin goes). This similar thing was used to allow ghasts to spawn in the nether.
Also, these legendary 'pokemon' would probably appear more as 'roaming pokemon', but instead of catching them, you 'kill' them. Pretend that killing the 'boss' mob acts as a pokemon fleeing battle and must be found elsewhere.
If these are given extremely small spawnrates, but extremely high health/attack damage (perhaps not overpowered) they could act as legendaries.
Another possibility for the legendaries that stay in the one place, have a script block walk event where that pokemon would otherwise be that will spawn one of these 'boss' mobs. Of course, a high delay on activating the scriptblock would have to be put in to prevent abuse...