Q: Why are the collector numbers for duel decks by deck and CMC instead of the usual WUBRG order?
A: From Del Laugel, Head Editor for Magic: The Gathering
As you know, the collector numbers in the card sets for major releases follow an established pattern: all white cards in alphabetical order by English name, then blue, black, red, green, multicolored, colorless artifacts, nonbasic land, and finally basic land cards. Sometimes judgment calls are required for a particular set. For example, Rise of the Eldrazi featured a number of high-profile colorless cards like Kozilek, Butcher of Truth. I chose to put those cards first when assigning collector numbers, in part to keep them away from the artifacts.
This traditional "WUBRG" ordering was chosen with nine-card binder pages in mind. If you put cards 1 through 9 on page one, and so on, you end up with a set that's ordered in a way that facilitates the building of decks. It's not a perfect system for a global game—collector numbers are the one constant across all languages—but at least all the green cards are together.
But your question was about the Duel Decks. The collector numbers in a Duel Decks product correspond to the order of cards in the deck lists printed on the strategy insert. This ordering is still intended to facilitate the building of decks—but in this case, the people building the decks are our print vendors! This system makes it much easier for everyone working on Duel Decks to spot and correct errors.
The decision to number Duel Decks in this way has a fortunate side effect. It encourages us to select unique basic land cards for each deck, even when they happen to share a color. This helps to give each deck its own distinctive identity.