I think how each inventory is best organized varies from person to person.
All of my items are organized by theme, type and color. But sometimes I need to use other criteria.
For example, if the theme of the item is horror, and I mostly use that item for horror avis I place it with other items I use for horror.
But sometimes an item may have a theme but the pose I use the most isn't very theme specific. In that case the most commonly used pose will determine where I put it. For example, Donna del Carnevalle: the icon is a crown so it goes to the hats tab and the overall theme of the item is Venetian cosplay, however the pose I use the most from that item is the hair and it's not exactly theme-specific, so the result is I didn't place it near the other crowns in my hats tab nor near the costume sets, I placed it near the other hair/wigs.
Items that I use all the time are the first in each tab so I don't have to scroll down for them.
After that I try to organize items first by theme and type of avis I use them for.
I look at each item and I determine which is the the post that most likely will lead me to the item, then I decide if I'm going to place it near items of the same theme or with items that defining pose best combines with. For example, In the Ruhk is mainly a background item, but the pose I'll most likely need to use from that item is the fire stick, so instead of placing this item with the other backgrounds I placed it near my lantern and candle items.
If the item contains major modifying poses like arms or legs I try to keep them together regardless of theme, so for example in my tops tab I have In Silence I kill, In Silence I Judge, Flight of the Highwire, Black Swan, White Swan, Fairy Lumi, Onyx and Ivory Trapeze, and others... all together so that when I need legs that are in items whose icon is a top, I'll know where to find them.
The whole process is so personal though, because it's really about how you would classify items first in your head to know what to look for and how to find it easily when you need it. To determine which poses define the type of item and the type of avis you use it for helps categorize things and organize them more efficiently.
After organizing everything I don't think I find the inventory arranger that frustrating, but the things is I did it little by little. If I were starting out to organize everything again I think I'd be pretty frustrated. I think the best advice is to plan first how the items are to be organized and then do a little everyday. Once an entire tab is done move on to the next. When all is done it'll feel really worth the trouble, especially when making new avis.
If Gaia could improve the arranger it would be great, and I wish they would allow users to create custom tabs in dress-up.