The lack in ease of reorganizing and reordering is my biggest issue and largest frustration.  I admit to being organizational-anal.

What would help tremendously is something on the order of an "export categories" "import categories" feature. There are so many things that aren't where I would like them, to try and reorganize everything in the interface is massively confusing and really time consuming (plus when I totally screw it up the reset throws a lovely error which I will put in a separate ticket). I'd like to be able to suck the categorization data into a spreadsheet, database or editor and do the adjusting there before exporting it back to TBag.

I have 9 90s with more on the way and they pass stuff back and forth daily based on who is farming what, who is making what, who is cooking, transmuting . . . This style of inventory management allows me to have about 60 empty slots in my bags most of the time.   Getting through the farming and Timeless dailies for that many 90s makes good organization vital.  

Everything that teleports the toon should be in one spot . . . the Stormwind Cape, the Timeless trinket, the hearthstone . . . That's a combo of where an item is located (which bar) and how the categories are set up.
Everything that's only a buff usable on Timeless Isle should be in one bar.  At 90, we spend a goodly portion of our play time there.  It makes sense to consolidate and isolate those buffs.
Everything that's a Pandaria only buff, with the exception of the above, should be in one bar.  All other buffs should be in a separate bar.  This would be a huge help for new players and they could see at a glance which buffs they can use in different locations.
And just a side note, having the underwater breathing potion in one bar and Nagrand cherries in another bar when they both do the same job is insane.  When trying to find something in inventory it makes no sense to have two things with the same effect in separate places.  That's an item categorization issue.

I want the scrolls and equipment for enchanting with the enchanting mats.
I want the parchment and ink kit with the inks and pigments and a separate bar for herbs.  Not all herbs are millable.
I want refined ore (smelted) separate from the non-smelted.  Not all ore gets smelted, some of it gets prospected.
I want one bar for each profession with the exception of mining which should only have unsmelted ore.  Kyparite would be in a JC bar, not the mining bar.  Getting this properly set would take some tweaking which further supports my plea for a way to more gracefully and efficiently make changes.

There's so much stuff that's pre-pandaria that no longer needs a bar of its own . . . all that stuff could be jacked into a single pre-panda bar if it could be done quickly and easily.

If Tbag came with a generic and logical setup that could more easily be tweaked . . .