Zappo
Explorer
I, too, think that if you want to make an RPG which uses Magic cards as resolution system you should take leave of D&D (and d20) entirely. Here's what I would do, if I had the time and will to embark into such a project:

- The characters are planewalkers. Not much sense otherwise. This obviously makes for a truly epic game!
- Make the game diceless. You don't want to have two radically different systems in your game; find some way to use the cards as action resolution for everything. Normal combat, in addition to spell duels, would work as the card game. Appropriate spells can be used in non-combat situations as well. Non-combat situations that aren't handled by magic are solved through roleplaying alone or through some very simple card-based mechanic. You could associate the type of actions to colors or types of cards, assuming that a wizard with lots of interrupts and green spells in his deck will be good at reflexes and wilderness lore, for example.
- Make the game classless. The character's role is determined by his deck; magic is an aspect of personality and abilities and vice-versa.
- Determine parameters which are used for character advancement, and a way to increase them with experience. Deck size, maximum number of copies of one card, hand size, that sort of stuff. Don't use things such as "maximum number of different colors" or "maximum mana cost"; as any experienced player will tell you, those are largely irrelevant for many deck types. Stick with stuff that is useful for almost everyone.
- Find a way to tie the Magic game rules to the game reality. What is a land card? Is it a character's holding? A mystical link to the earth? How do you carry it around? How long does a game turn last? One round, one day? What do your "cards in hand" represent, and what does your "library" represent? Why are my cards in hand random? What does the graveyard represent anyway?