I've been looking at/trying to develop a color based spell casting system since before the first free Planeshift document came out. Everything has warts. Literally a square peg into a round hole.Likewise. I haven't seen a color-wheel based magic system yet that models the card game well. I think WotC's decision to effectively ignore the color wheel in their D&D/Magic crossovers is the best choice yet. It's been a while since I've read any Magic lore (novels, webstories), but I'm pretty sure the idea of a "blue mage" isn't really supported in the fiction either. Which mana colors each Planeswalker or magic-user has affinity towards seems to be behind-the-scenes type of stuff rather than explicitly the way characters see magic in-universe.
Not a workable system, but the best attempt I've seen is Spell List as Color by Laurafindel is a good base to build off of. She just takes all the existing D&D spells and divides them by color. The colors are not balanced against each other in any way, just dividing spells by color instead of class.
I do agree that WotC ignoring the color wheel for magical effects is probably the best choice.
I am going to check out the link that dave2008 posted on the DMsGuild.