Well it depends what you mean by a better footballer. Obviously there are certain attributes that Anderson has, Cleverley does not have, like running with the ball and beating a man. But I'd say that Cleverly has better positional sense and is tactically more astute. I think the team is more effective and solid with Cleverley partnering Carrick then Anderson partnering him in a 2 man midfield.
Anderson has had 6 seasons to establish a first team spot at the club where for long periods Hargreaves, Fletcher and Scholes have been either injured, or retired. The fact he has failed to so, despite United having not bought a midfielder since he was bought, is the reason why United are looking to bring in 2 midfielders in the first place. It's not a matter of prioritising over someone from the academy over someone who was bought for around £20m. The simple truth is that Cleverley has been more consistent then Anderson and had had longer periods of being fit then Anderson. You can look at it from a more gloomier angle and say that Cleverley is a less worse option then Anderson.