Pokémon has put itself in this spot where if they have an uncatchable creature it would feel rather off-putting, like "hey, I can use the rulers of time, space, antimatter, and the beast who created them all, what's an alien to me?" I do agree, however, that they should have been more challenging to obtain, something more plot-centered rather than treating them like generic wild Pokémon.
I think the real major missed-opportunity was not having Corrupt-Lusamine be her own Pokémon in battle. It could have opened up the possibility for a really unique boss fight. I feel her being a combination of Pokémon and human would make it more sensible as to why she couldn't be captured, only fought.