My suggestion is simple, a backpack, like they have in the pokemon games (heart Gold/Soul Silver mainly) for holding the item for pixelmon exclusively.
basically the pouch will automatically take the pixelmon items from the player inventory and assign them to the their respective slots, pokeballs, TM/HM, etc. which would still be accessible by the player either through an assigned key, or an icon in the players regular inventory, so they can access items used in crafting recipes or use items on their pixelmon, either directly from the backpack like in the games, or the way that they are used now.
the bag itself would need to be crafted, and could be stored in a new equip slot on the player like the baubles mod does, and would be visible on the players model.
like the games the bag would technically have unlimited storage, being limited to only 1-99 (or 64 if wanted) of each item ( again, it can only hold pixelmon items) ultimately giving the player more inventory space to collect the random things that catch his/her fancy while adventuring.
limit 1 per player wearable at a time -- items stay in the backpack when it is removed or stored.
**Optional thought**
could also have teirs for the bags, so small teir only has room for 10 items, medium 25, large 50, and ender - unlimited
Cheers,
Shaduun