I installed the eStore plugin on my wpmu site and it overrides quota. The creator of the plugin was kind enough to take on my suggestion to set the eShop quota to the one you choose in the admin panel.
But here's something that I would like and I would think others would like as well: The opportunity for users to buy more quota.
Ofcourse this can be handeled manually. But it would be dope with a paypal system where you set the price/mb or /10mb and blogowners can pay to get more disc space. It wouldn't just apply to people wanting to sell downloads, but "normal" users that are posting images, music etc would probably appreciate the opportunity to get more quota as well.
So that's my suggestion. Did some googling and it doesn't seem to be working.
There are probably other extra features that you could charge for, but disc quota is the only obvious thing I could think of.