Jones has played next to Carrick before and it's looked fine, QPR and Villa away last season IIRC, think he might have scored against Villa. But anyway, he was bombing forward making those runs he does and looked great.
It was different today though and I get where you are coming from, he was much more reserved and clearly defence came first, instead of the box to box role he has played in the middle previously. Point is that I think this was tactical rather than anything inherently wrong with the partnership, Fergie must have wanted cover for Mata or something because he's played a centre mid role more expansive in the past.
Can see where you are coming from with your comments on the passing though, Carrick can fizz it into feet but from the distance he plays at he isn't going to be hitting through balls for Hernandez much, simply because he's too far away. It's no slight on him as a player or his passing, just the position he plays in the team.