I'm doing just fine with inventory management. You have to use both retainers and sort everything as it goes into storage. I sort things by type. I keep all my crafting materials obtained through combat on two pages and even keep different skins/hides grouped together. I have 2 pages for materials I mined with ore in one place and everything else separate. I use three pages for botany - one for wood and two for foods. My other retainer holds onto intermediate crafted goods like leather and ingots, materia, and gear I'm not currently using.

My only problem, as someone else said, is the armory chest. A simple "sort by level" function would vastly improve the functionality for me. The constant switching between classes makes the whole thing one big jumble that's impossible to keep sorted properly on your own.