Honestly, for a narcissistic character like Jack who can rarely admit to his true feelings, this is sort of a perfect ending.
So, A.P. Bio ends with Jack stammering and flustered, already worried about making the choice between staying in Toledo for Lynette and taking off for greener pastures when he gets his book published.
His life, with or without Lynette, with probably always be filled with dilemmas like this, so, while it doesn’t exactly give fans closure, at least we know Jack will always be Jack.