I think Skywest would pay less if they acquired post bankruptcy as the only way a judge and the creditors committee would approve an outside plan that involved liquidation is either if Mesa's POR was complete crap or if the payout was more (a good deal more) than what they could recover in Mesa's POR.
But then again maybe not, obviously JO would have no job post-merger and that might be enough to cause him to torpedo a post-BK merger, he is a felon after all.