I'd much rather see the export feature implemented first, but i think this is an important feature as well.
Are you planning on allowing an "Unspecified" subset as well? Once you open this can of worms, unless you add an "unspecified" subset, you're going to have to deal with every single variant, like promos, Championship decks, etc etc.
I'm wondering, as you enter the cards, are you going to have the page automatically calculate the valid subsets for a given card? In other words, exclude any sets that the card did not appear in?
I don't think giving users the ability to create subsets is a good idea, simply because there will be misspelled and duplicate subsets, which will make things confusing while searching later down the road.
As for my ideas:
For adding inventory via the auto-complete box, I think the easiest way would be once you type in your card, it auto-completes, you pick the card you want and a drop-down box with the subsets is displayed automatically with a quantity box beside that, then a button to add an additional line with another subset drop-down box and quantity box for additional copies, then another button to add an additional line, etc etc. That way you can keep adding cards from different sets without every having the re-choose that card.
So it would be like this
[Auto-Completed_Card_Name_Selected] [Auto-Complete_Subset_List] [QuantityBox] [Add_Row]
[Auto-Complete_Subset_List] [QuantityBox] [Add_Row]
[Auto-Complete_Subset_List] [QuantityBox] [Add_Row]
.........................
[Auto-Complete_Subset_List] [QuantityBox] [Add_Row]
Another alternative would be to just have all the subsets listed once the card is auto-completed plus an "unspecified" subset, like this:
[Auto-Completed_Card_Name_Selected] [Subset1] [QuantityBox]
[Subset2] [QuantityBox]
[Subset3] [QuantityBox]
.........................
[SubsetN] [QuantityBox]
For in-line inventory additions using the full card list, you can have collapsible inventory rows (think the windows explorer tree folder structure, but only two levels) that have a + out beside each card's row. Clicking the plus will display all the subsets a card is in below that card's row and tabbed over to the right a little, then you can add cards or requests using the columns there. If someone adds inventory without expanding the the row, then the cards are added to the "unspecified" subset.
So this one would be like this:
Inv Trade Wish Card Name
[+] [ ] [ ] [ ] Card 1 <----- Entering values into this line would add a card to your inventory with subset "unspecified"
[-] Card 2 <----- Notice the + turns into a - when clicked. Clicking the - will collapse the tree, while clicking the + expands it
[ ] [ ] [ ] Subset 1 <----- Each of these N subsets are the only subsets in which Card 2 appears in
[ ] [ ] [ ] Subset 2 Entering values into these lines will add that quantity to your inventory with that subset
[ ] [ ] [ ] Subset 3
...............
[ ] [ ] [ ] Subset N
[+] [ ] [ ] [ ] Card 3
Then to top it all off, have the ability to view all cards in the unspecified subset in your inventory so you can have a easy to way to go back and change them all without trudging through the rest of the your inventory.
FYI, I know like bare-minimum php, so I have no idea how hard this would be to code. But I think it's all do-able, just (probably) VERY time-consuming.