There's plenty of excellent points made by the opening post of this thread.
I'm in agreement that the "Greater Anglia" franchise should encompass NXEA, C2C (Which is intended to be the case already isn't it?) and the parts of the GN that won't be consumed by the extended Thameslink operation, which primarily consists, AFAIAA, the longer distance Cambridge services being proposed to be worked by IEP trains.
I'd very much like to see the fourteen 332s moved to Northern to join their 333 bretherin and allow the 321s & 322s to go to Anglia, though as others have stated I'm not sure how easy this would be with their different lease arrangement to the majority of other stock. Perhaps this would be possible after Crossrail is launched if that service was adapted to serve the Airport.
Virgin should certainly receive enough additional Pendolinos to at least cover the Birmingham to Scotland route, and maybe the London to North Wales services as well, with infill electrification as far as Chester. Continuing the Pendolino build to 390072 should be sufficient to cover both of these routes and allow VTs' 221s to go to XC.
If Chiltern were to be merged with anyone, other posters have convinced me that it would be best for them to be absorbed into the FGW franchise. Though in the medium term Chiltern taking over the Snow Hill lines local operation would be an excellent idea.
London Midland would sit best with the West Coast franchise if it were absorbed, although this raises questions over whether the Birmingham to Hereford/Shrewsbury and Cross City line electric services would be better placed with an expanded FGW operation if they absorbed Chiltern, or with the West Coast franchise.
As for Pacer replacement, especially concerning Northern, I am wedded to the idea of extensive electrification projects, although I admit this is probably not realistic within the available timeframe when the currently announced electrification projects that are going ahead take us up to almost the end of the decade already.