I played a D20 Mutant Chronicles one shot at a convention and the GM just spliced 3e D&D with SpyCraft. It was a little wonky because the gun range made sword skills kinda useless. The minis looked great though!
The other odd issue was the MC knowledge of the players. Some of us came from WarZone, some from Doom Trooper, some from the MC RPG, and some from Siege of the Citadel. The effect was odd since the canon presented in each iteration of the game was somewhat different. Akin to the difference in Warhammer if you came from Fantasy Battles or from WFRP 1e or from Warhammer Quest.
I am unsure how I would convert MC, but first I would set down what is going to be "canon" in my MC campaign and see how I wanted the world to be and then mold the system to my desire. These days, I would probably use the new Gamma World because it would be quick & dirty and the danger level in combat fits the MC world nicely.
That's not to say that Modern D20 or True20 wouldn't be equally good, but I like fast PC/NPC gen and brutal combat.