To bring this back to it's original point. Yes the franchise will not deliver transformational infrastructure, there job is to 'tart up' existing stations not to overhaul the railways. Therefore what is the transformational infrastructure that is needed? within the bounds of reality.
As a Merseysider I hate my first suggestion, but
1. Does Manchester need to become the centre of Northern transport beyond the current hub project? By this I mean the London model. If you arrive in London on an intercity train you have to change to go anywhere else. So in Manchester you build the Ordsal chord and Re-instate the Blind lane but with a chord on a flyover to go south to the Airport and Run an MIA - MAN - MCO - DGT - SFD - MCV - SPORTCITY - MIA regular clock face service in either direction / one direction. No one would get a direct airport connection except the people on the route between Wilmslow and Levenshulme? Effectively creating an overground circle line. The trains would be at a similar frequency to the London Underground. 3-5 minutes. (i.e. just Enough time to reverse them at the airport and making them the only trains using the Piccadilly - Victoria link.
1b Alternatively Do all the Manchester stations need to be combined into one mega station with terminal and through platforms in every direction?
2 Do the main lines between all the Northern cities (Manchester - Leeds - Sheffield Triangle, Man - Liverpool, and Sheffield to Newcastle via Leeds) all need to be four tracked.
2b Could this be combined with clock face stopping Metro services that interface rather than intertwine. For example Merseyrail and Metrolink extend to Warrington Central, Newton le Willows, Wigan and Preston. With a similar central focused metro around Leeds and Sheffield (Splitting points are less obvious but you get the idea.)
3 Pause HS2 Phase 2 when Crewe is joined up and Focus on a 'HS3' with stations aligned for Optimum inter connectivity for the North maybe Sheffield to Newcastle with a Liverpool to 3 way junction somewhere near Barnsley and a branch to Liverpool via Manchester. HS2 could then continue roughly as intended to Sheffield and extend from Crewe to join the Manchester - Liverpool Branch.
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The MSJ&A line from Piccadilly to Knott Mill was not designed for and is not capable of taking all the traffic (including freight) that some people wish to route via it. Unfortunately, routeing trains via the Ordsall chord (now under construction) from Victoria to Piccadilly will exacerbate the problem.
Agreed, particularly the freight it never ceases to amaze me standing on a very crowded platform 14 at Piccadilly and seeing a freight train go past. I don't know where this is going from / to but find it incredible that there is not a bypass. If MSJ&A didn't already exist you certainly wouldn't design the Ordsall Chord like this.
It is not physically practicable to quadruple this stretch of line.
Not in the realms of finance for Northern Railway projects. Maybe if it was joining Kings Cross and Victoria. I had always wondered, (if money and disruption was no object) if you could completely knock down the viaduct and rebuild it as a double deck 2 track. But yes I agree its not likely.
More use should be made of Victoria as the main station for trains on the LNW Liverpool-Leeds route as well as most services from the north side of the city.
In addition, no trains should run from the ex-GC lines across the Piccadilly station throat to the MSJ&A line. All diesel trains from the south and east should run into the terminal platforms at Piccadilly.
If I understand you that has the effect of stopping the Cleethorpes train extending to the Airport and the Nottingham-Norwich Train continuing to Liverpool. I have very mixed feelings about this I spent 4 years of my life in Sheffield and those trains particularly the Liverpool one where my lifeline. Given all your trains that are going from North West places to Victoria, having trains to major places to the South East where you have to make multiple changes in Manchester is exactly the kind of thing that stops you travelling by train and puts you in a car.
I think as a general rule of thumb most users across the North would expect every city to have a direct connection to every other. A provincial towns eg Warrington, Bradford, Blackburn, Burnley, Wakefield, Barnsley, Middlesborough Scunthorpe, Doncaster, etc should have a regular service between each other by a maximum of two connections, and have access to each of the Northern cities by a maximum of one, I think the East Midlands - Liverpool service caters for a lot of those. Certainly cities the size of Liverpool and Sheffield should have a direct connection between them.
I don't know about the airport. I have to be honest I have only once got a return train journey to MIA. I would love to use it more, but most of my travel recently is business and they put a Private Taxi for us. Also whilst there might be early/late trains between the cities and the airport, there are rarely trains running early enough to get you from the outlying towns to one of those trains or late enough to get you home. What I do know was that the day I tried it, there had been some cable theft on the route and the one direct train I had planned to get was cancelled. I just made check in for the flight because I now had to make 2 connections, one to get to the right Manchester station as the next train went to Victoria then one at Piccadilly. It was incredibly stressful and is probably what puts me off doing it more. Many people claim it is for the baggage that make people want a direct connection when actually I think it is the increased stress of potential missed connections and thus your flight. The chord will do a lot to help this as people will now only ever have to make one connection and if you are delayed there will be plenty of other services to the airport it won't however help with the early departures and late arrivals.