Yeah, but all you would need is some sort of way to "lock in" people's secret bases so they aren't overwritten, or at least some sort of "this will be overwritten" notification (AKA, don't do what Mario Kart 7 does where you have no control over what gets deleted). I think the biggest impediment to Secret Bases in Gen III and IV was just the whole lack of connectivity and no one really ever had a chance to use them to their full extent. Streetpass kind of totally changes that and I think it'll be a huge shame if Game Freak doesn't take advantage of it.
I guess the biggest question is: what's the limit on data that can be sent through Streetpass? Is Pokemon team data, trainer information and secret base location/layout too much data to send at once or do I vastly underestimate the little machines we carry in our pockets?