Just can't see this working as a long haul connection route and it is a fantasy to consider it could. It will take time to build up passenger numbers but with Crossrail opening next year Heathrow will be a more versatile option for most with trains running every few minutes rather than hanging around for a flight connection at Manchester.
Remember Shenfield to Heathrow will be only a 75 minute journey, which will be quicker than checking in at Southend and waiting for the departure and that is before you add the flight times which will show as an hour. Also can't see a Southend air route competing on fares with a cross London rail route so forget the long haul option.
There might be a demand for a Manchester service for people wanting to go to the North of England on business but I would think there would be more of a demand for an Edinburgh domestic service for no other reason than it is a lot further away.