Eh... now this is excessive complaining IMO. FFXI players complaining that ammo only went to stacks of 12 originally was a valid complaint. Needing more than 99 per slot, is asking a bit much.
I don't see how you can possibly feel the inventory system in its current iteration is adequate in any way. We will just have to agree to disagree.
...Most other MMOs I've played have had drastically higher stack limits for things like ammo, in the range of 999, 2000, etc. 99 is remarkably low, and really only existed because of the limitations of how the AH worked in FFXI. If you wanted to sell more than ONE item at a time, it had to be a full stack. You couldn't just take 8 of something that stacked and put them all up on the AH at once, demanding a certain price per item. For this reason, it was impossible to sell drastically large sets of arrows or bullets in FFXI because you only got to sell all or one at a time... Knowing this limitation, FFXIV could take the opportunity to not make the same mistake. Since there is currently no AH in place anyway, there's really no reason to make ammunition stack to only 99. Right now it's completely arbitrary, so why implement it that way? There has to be a reason for it now, and "FFXI did it that way" isn't legitimate.
Greg Street (google him if you don't know who he is) referred to things like this as 'quality of life' changes for players - things that did not affect game balance but simply made the playing experience more streamlined and enjoyable and removed unnecessary hassle. I'd love to play the game more and the UI less. I really would.
Given the lack of inventory space and the absolute necessity of leveling multiple crafts simultaneously, I'd think that effective inventory management would have been very important to the design team. Shows what i know.