I bet you could delete phone numbers using that save file program thing... but it wouldn't work for those that aren't playing on a flash cart (which is pretty much everyone because of the Pokewalker).
The only other solution is restarting, which if all you did is the main quest, a good opportunity to try using an overpowered team early on and see how fun it is or something.
Edit: I didn't even take those guys' phone numbers because I thought they might call me every second to give me a repel or a potion. I decided that once I'll finish the league I'll go back and get all of their numbers again to get free stuff, now that I know they're good things like stones and berries.
The only other solution is restarting, which if all you did is the main quest, a good opportunity to try using an overpowered team early on and see how fun it is or something.
Edit: I didn't even take those guys' phone numbers because I thought they might call me every second to give me a repel or a potion. I decided that once I'll finish the league I'll go back and get all of their numbers again to get free stuff, now that I know they're good things like stones and berries.