I think that makes the most sense to me, so thankfully with this game still in its beta phase there's always a possibility for change down the road.
Another thing to keep in mind though, is that I'm sure there are only so many similarities this game can share with the games directly affiliated with Nintendo, so the decision to keep the legendary Pokemon almost completely uncatchable may be for various reasons that extend beyond what would just be cool in the game. Who knows though :)