I honestly don't see many negative consequences to allowing you to buy partial stacks. Seems like most that are against such an addition simply don't want it because it's a change. While it means that single high priced items won't sell, it's more convenient for those that have a lot of different things to sell (you can only sell 20 items per retainer regardless of quantity unless it's more than 99) as you don't need to wait for someone who needs a high number of materials, and makes it easier for people to buy the number of items they need instead of server hopping or reselling because there's only stacks of 99 available when they only need a small amount.

All they would do is add a feature that allows you to pick how many of an item you would like and it would buy them starting from the cheapest stacks first.

For example, need 12 logs to make a bow? The game will buy the stack of 5 for 300 gil, 1 for 350 gil, 3 for 398 gil, 1 for 399 gil, and 2 from the stack of 99 for 400 gil.