My first take on a quick-and-dirty Magic: the Gathering RPG aimed at playing Planeswalkers would be a Nobilis conversion with the five colors as your ability scores. If I deemed the "land generates mana" mechanic of the card game something that should be reflected in the reality of the world, then I'd introduce some kind of mechanics where you need to ritually bind locations to achieve regeneration of miracle points (which would be renamed to Mana). If I wanted to keep the "start small and work your way up to big effects rule", there would need to be some sort of mechanic that required the links to lands to be brought "online" somehow, with some kind of a fatigue system to explain why you don't keep them up all the time. However, that leads to the obvious tactic of ambushes—one Planeswalker wanting to take out another would bring up all his lands, then jump the other guy, so clearly bringing up lands is an Exalted-anima-flare-level signal crossed with In Nomine Disturbance that alerts all other magically-capable beings within miles that serious crap is going down, and maybe they should start powering up too, just in case.
For something more detailed and custom-made, I'd start by mapping colors to attributes. Taking the original White Wolf 10 (3x3 Attributes plus Willpower), I'd dish them out something like:
Red = Strength + Agility
Green = Stamina + Wits (not too keen on the latter…)
White = Charisma + Appearance
Blue = Intelligence + Perception
Black = Will + Manipulation
Additionally, I think each color would need some virtues that it feels exemplify its philosophy:
Red = Might & Courage
Green = Fortitude & Nurturing
White = Duty & Order
Blue = Cunning & Restraint
Black = Pragmatism & Resourcefulness.
Then, on top of this, I might add a skill system, then in plug some kind of resolution mechanic. Under this approach, spells are probably best explicitly known, allowing the acquisition of new spells, analogous to getting new cards, to be a focus of play. The spells themselves should probably be built with some kind of underlying mechanics for consistency, so it'd be somewhat Mage-like with a focus on Rotes. Maybe you can perform free-form magic too, but it should be much harder or more expensive than a known spell.
Alternately, we could define the whole setup in terms of pairs of colors, highlighting what each has in common with its allies and enemies, which may let us better model the modern color pie:
Red & Black = Agility, Victory
Black & Blue = Manipulation, Resourcefulness
Blue & White = Intelligence, Restraint
White & Green = Appearance, Nurturing
Green & Red = Strength, Might
Red & White = Charisma, Courage
White & Black = Will, Sacrifice
Black & Green = Stamina, Fortitude
Green & Blue = Perception, Vision
Blue & Red = Wits, Cunning
I think I like this latter approach better, but then I'm a sucker for complex symmetric structures.