I think Miami has invested enough time in Thomas to think he's anything more than what he's given you. A RB's game isn't so much different from one offense to the next, there's nothing groundbreaking about what Miami will do running the ball that suggests Thomas has been in the wrong system or used incorrectly. He's a big back that runs like a small back and no amount of spread offense theory will fix that.
Is Williams the man? Probably not, but he's got potential, youth, and isn't trying to be something he's not. Cut Thomas, keep Williams, I don't see how the decision could be anything else.