Deck-Editing
Magic players universally hated the original Duels of the Planeswalkers deck-editor because it wasnt really an editor. It allowed you to add unlocked cards to your deck, but you couldnt pull cards out.
Highly annoying.
This was the first improvement that I recall Paul pointing out to me. Now players are able to have full control over the non-mana cards in their deck. So, as you unlock cards, you can slide them into your deck and pull out another card. The game does not yet allow you to mix and match cards from different decks, though, so you cant mix Koths and Chandras decks together even though theyre both mono-Red.
The deck-builder also still manages your lands. It calculates what you need based on how many cards youve picked for your deck. So you cant specifically cut an island for a White card, but its going to programmatically determine that for you.