Here are my suggestions for fixing the inventory system:
1. Replace the current vanity system (glamour) with Wild Star's vanity system. In it, you find an item and then save its appearance. Afterwards you can throw out the item because you don't need the physical copy of the item anymore. No more wasted inventory space holding old raid and dungeon sets. Just a nice, simple GUI to select what a person wants to wear and presto.
2. If an item constitutes a form of currency of any kind, it goes in the currency tab, not an inventory space. I'm looking at you, ancient ambers. The Alexander items would also constitute a form of currency.
1+2. Glamour prisms, clear prisms, etc go in a vanity currency tab.
3. Dyes should be one time consumables. A player uses one and now they have the color unlocked. To change the color of a piece of equipment, they must have a special item that counts as a form of currency and goes in the currency tab. Either that or create a dye tab. Dyes take up a ton of unnecessary space in the inventory and are a poor choice as a consumable because there can be an almost infinite number of different colors to choose from (its all on a gradient, after all).
4. Gyshal Greens, while not currency, should probably go in the currency tab or some kind of companion tab.
5. Fishermen bate should go under a specific section in the currency tab, as they are expendables and have about as many divisions as their are different colors of dye. Well maybe not that many, but still enough to cause inventory issues should a fisherman carry a full compliment of both fresh water and salt water bate.
6. Seasonal and event items that are not a form of currency, but are used only for quests should go in the quest items tab. An example of these would be the "queer garb" items from the Lightning event. I was confused into thinking that the queer garb items might play into some kind of crafting recipe when those events first occurred, leading me to store those items for later. Best not to leave any shred of doubt as to their purpose and put them in their proper place.
7. Seasonal and event items that are used as currency and intended only as currency should go in the currency tab.
8. Avoid giving out "free pass" items like those 5 free mini game passes at the gold saucer. Some people complete the quests, don't know what to do with those items, and then hold onto them for a while. So they end up wasting inventory space. Instead, they should act as consumables that grant whatever currency is needed for the area.