Don't know if this has been suggested yet, so I'll post it here.

Honestly what they should do is allow people to sell as a stack as a choice. If you have less than 99 of an item, then buyers should be able to buy single from that number. So basically stacks would be in its own category, much like HQ's can be sorted and searched for separately. If I'm not mistaken, 1.0 was like this somewhat. Simply just add the option of stacks as an advanced search term, or (for items that apply) give an option when you click on it, for stacks and single items.

Essentially this will create four different markets for competitive pricing, the stack price and the single item price and the two HQ versions....so HQ stack and HQ Single.

I think this will improve the economy so that pricing might be a bit more fair and people can actually make some decent Gil.