Simply changing Genesect to a non-legend is not really going to cut it imo. It's been established canonically to be legendary. And even if it was common; it's an extremely powerful Pokemon on par with the other legendary Pokemon too, and as it's hinted there's only one of them made you've going to either really have a really good explanation/s for it or have to go with some reader disbelief. 'In this context' doesn't explain it yet because...well, it doesn't make it clear in the story (something Astinus stated earlier) and I've no idea how it could be not classified as at least a rare unique Pokemon if not legendary (which it is canonically).
As for explaining later... well, that's another risk. That may be true and all but I'm already wondering 'why is ____' for many things, and for there to be so many currently unexplained to the degree of there being an alien with connections to two legendary Pokemon, an out-of-character Oak and so forth I'd be wary of leaving too much for later.