I'd like to see the ability to define which edition of a card you're using in the deck. Right now, if you display the edition column in the deck view, it seems to list the 'newest' edition of the card, regardless of what's in the inventory.
As an example, I made a deck that has 3 Forests in it, without any Forest cards in my inventory. The edition was listed as Innistrad. (The most recent set is Dark Ascension, but DKA packs contain ISD basic lands.) I added 3 Zendikar Forests to my inventory, and now the deck view doesn't complain about the fact that I don't own the card, but it still shows it as Innistrad Forests, despite my inventory only containing Zendikar Forests.
That by itself is a disconnect. More importantly, however, I'd like to be able to specify exactly what edition is in my deck, regardless of what's in my inventory. For example, I own Confiscate in several different editions. Deckbox defaults to Ninth Edition. Seventh Edition, Eighth Edition, and Ninth Edition versions of Conficate have white borders. Urza's Saga Confiscate has a black border. In one of my decks, I've gone out of my way to ensure all of the cards in it are blackbordered, so I want my decklist to show the Urza's Saga Confiscate, but instead it shows Ninth Edition.
Additionally, it would be nice to be able to specify which art for a given card we have (both in a deck and in the collection). A few Magic sets have cards with multiple arts within the same set. (High Tide 1, High Tide 2, High Tide 3 from Fallen Empires.) In some cases, one of the arts was even a different rarity from the other versions of the same card (Mishra's Factory (winter) and Strip Mine (tower) are both Uncommon, while the other three arts were Rare). Being able to separate these within a collection or deck would be a great bonus.