In terms of inventory space it is not hard to sort or look for things. The only annoyingthing really is when you have a FC vault , multiple retainers to call up every time. However these problems are really insignificant if you are organized. Here is my setup to make things very easy being I'm constantly crafting and taking advantage of the high demand for lower level gathering gear in my server.

Personal bag. Unless I'm crafting at the moment 0 materials( exception of gathering collection items ). Keep materia , support potions, and on only items that I have retainers gathering. Once I only craft I fully stock on items I'm focusing on and makes it a lot easier.

Retainers depending on their role they hold that type of item. Easy no problem finding it and when needed I know what retainer to call.
[B]
Choco bag; only for misc type items that I actually use. Scrolls, manuals, gear that needs to be enhanced, kind of a check of list.

Being people are also impatient when crafting and want to know exact location the search function works great, tells you what panel and slot. People can sort and un - sort, I'm just glad they allowed the 999 stacks now.

FC vault; Unless it's related to projects or completed parts no other real reason for it being used.

Over all slot inventories are a pain, however they are better than other types. I hate rotating inventories -.-;