Yes Heathrow is to be Britain's main alliance hub, but it is a very unpleasant airport. All I can say is that I hope Heathrow's improvements are good!
Having said that it's not difficult to avoid Heathrow and usual with better flight times, when I was working for a previous employer in Damascus I would fly in to Stansted via Istanbul with Turkish and it was often less expensive, I even convinced my company to do the same. It is easy for Manchester travellers to transit Newark, Atlanta, Paris, Dubai, Frankfurt, Abu Dhabi, Singapore, Istanbul which brings us to the stumbling point for a lot of the alliance airlines:
Why on earth would UK regional passengers make TWO connections (e.g down to Heathrow on BMI, Chicago on United and then on to your final US destination) when they could go to Newark and make the short regional flight from there. A lot of passengers search on price so in order to entice passengers through Heathrow instead of EWR or CDG those had better be low.