The fresh start idea has less to do with being able to transfer BEFORE you get the national dex and more to do the game mechanics. Some people want the IV system and other aspects of the game changed, and they believe that bringing over older Pokemon is what is keeping the system in place.
I mean, it's technically a fresh start each gen anyways since you aren't allowed to transfer before you beat the game anyways (Crown Beasts and Celebi in gen 5 notwithstanding). So the only reason to not want transfers, aside from hacking, is for a refresh of the system- rework the mechanics like when we jumped from Gen 2 to Gen 3.
I honestly wouldn't mind if we didn't have transfers, but I can see why it'd tick people off. Personally, if we did have transfers, I'd rather see effort go into a 3DS app that's basically like Pokemon Box- you can dump your Gen 5 pokes onto the box, and any of the gen 6 games you have can access the box.