Having thought about it, this is what I'd do:
LONDON
-Send HS2 into a rebuilt (again) St Pancras station, eg: a two level station with HS2 underneath the existing station. This could also result in more platforms for the MML.
-On the approach to St Pancras, build a new connection (double track) between HS2 and HS1, allowing through journeys to both Kent and Europe).
-At Old Oak Common, ensure that there will be good connections available to Heathrow with Crossrail.
-Maybe in the far future, build a new HS2-HS1 link via Heathrow AND Gatwick.
BIRMINGHAM
-Redesign the Curzon Street area so that: 1) a new station is built on the existing eastern approach to New Street for local (Cross City) and possibly residual intercity and CrossCountry services to call at. This would potentially involve building 2 extra tracks along the what looks like wasteland where I assume the new Curzon Street station will be built. 2) Build the new Curzon Street station so that there are some terminating platforms (lets say 4), but then there are another 4 that are through platforms that feed into the New Street approach for a variety of through services, eg: London-Bristol and Bristol-Leeds via HS2. (Looking on Google Maps, there appears to be sufficient space for this.)
-At Birmingham Interchange, ensure that there are good links to the airport.
EASTERN BRANCH
-I would keep the Toton Parkway station, but put in a connection to the MML near East Midlands Parkway, so that classic compatible services could run to Nottingham and Derby etc.
-In Sheffield, I would keep the Meadowhall station, but also include a classic compatible loop through Sheffield (that could possibly be used later for HS3)
-In Leeds, I would redesign the route so that there would be a new through station, through which all HS2 trains to Leeds and beyond would run, saving the need for both a connection to the ECML near York AND a terminal branch to Leeds (they would sort of be amalgamated into one).
WESTERN BRANCH
-I would build a new Crewe high-speed station next to the existing one, and put connections to the WCML at both ends so that services from the south could run on HS2 into Manchester, and services from HS2 could run to other destinations.
-I wouldn't make any further decisions about the route into Manchester until what form HS3 will take is known, because it would then be possible to join both together and have some sections of common running. This would also allow faster HS2 services to Liverpool.
-I would, however, ensure that a station is built next to Manchester Airport with good transfer links.
Hopefully, this would then entice road and air users onto HS2- for example, an international traveller flying into Heathrow would then, instead of flying to Manchester, would take the train instead.