Now that you have converted the offline RPG to an MMO, how about add certain features that are exclusive to an MMO like raids, like you as one player battle the legendary with your most powerful 6 Pokémon. This will also give the players some motivation to raise their Pokémon and use the less utilized functions like berry farming, etc . Why not implement those legendaries as highly buffed overpowered raids that players can defeat and obtain certain items or high amount of experience, but make them uncatchable. The game seems quite incomplete as there are only a few legendaries in it and that too you have to struggle to keep their possession.
Please think about this idea. After all PokéMMO is not the usual Pokemon any more it's an MMORPG now, I guess raid battle makes sense. We really need to bring those legendaries, even if you make them uncatchable is fine.