Personally, I would like so see it where you could get at least base set in a box. You could expand the set with different level cards (kind of like Black Diamond). Some people just want to try a single box of a particular product, so if it's a bit of a dud, at least you have the set. Or if you give away all the base to some kid, he'd have a full set.
There aren't many card shops around my area and few would carry base cards. I had one dealer pretty much tell me he's not interested in trading base unless it was 20 to 1. When I asked why, he said "it helps you", but doesn't do me any good". Plus I'm not a "big spender" at the shops so maybe in their eyes I'm not a worthwhile customer.
Or designate the box for base collectors (i.e. like Original 6). So for bigger sets, split up the base according to boxes. And it could be a mix too. By conference, or by division, CAN vs USA. Original 6. You could even list it out. 1-100, 101-200, etc.
So base collectors of a particular team can pick that box up and know that they're going to get all their base wants.
Nothing is more frustrating to me than getting 80% of one set and having 40% of a 2nd set in a box.