Firstly, existing mothballed rail infrastructure should
not be used for high-speed rail. This is reserved for local metro use, where it is of greater value to the people and city and in promoting economic growth. The city is expanding slowly and this expansion maybe accelerated once the depression falls away. The city was laid out to hold over 2 million.
I doubt HS2 and Merseyrail would share the same short stretch of tracks in the Victoria/Waterloo tunnel as high-speed rail is to be largely separate. A frequent stopping metro service will hinder HS2/HS3 trains of which there will a number of them at peak times entering the city. The Waterloo tunnel emerges at Waterloo Dock in Liverpool Waters. The large complex needs to be on the metro network and the tunnel is right there. The Royal hospital needs its own metro station. People from the likes of Wigan and Chester would have direct access to the regions prime teaching hospital, maybe with direct station access into the hospital itself - it is "their" hospital as well. The Royal is a specialist hospital not a local general hospital, needing top transport links all over the region. A station at the hospital is a priority.
20Miles, who I have a lot of respect, have largely hung their hat on using the Exchange station site using the eastern section of the Outer Loop and the unused Walton tunnels. They do all to divert from Lime St being used.
What is needed is to stand back and look at the whole picture and in relation to where the city is moving. The centre is moving onto the waterfront. The run down state of London Rd behind Lime St station is indicative of that. There are three locations in place for high-speed rail: Lime St from the east, Central from the south and Exchange from the north and south.
- Lime St: This site is near the shopping quarter and on the now edge of the city centre. Not as difficult as the anti-Liverpool people are saying. A dive under tunnel at Queens Dr is the only real major civil investment in gaining access, accommodating two Manchester/TPE tracks and two Merseyrail tracks, reinstating the 4 track at this point, so a win, win all around. HS2/HS3 can use the existing level tracks. Trains can be split in half and use two platforms - it is done elsewhere - which is far more convenient for passengers. Local urban trains can be diverted from the station to the underground section using the Wapping tunnel, releasing platform space. A travelator can be cut to Central station merging the two stations . I see they have installed overhead wire pylons on the unused trackbeds in the Olive Mount cutting. They will use this as an excuse not to make it 4 track in the cutting for sure. No existing, or future, local services will be impeded and would be enhanced by diverting trains from the east into the underground section.
- Exchange: This site is near the cruise liner terminal and right in the business quarter. This can be accessed using the original alignment from the north turning it back into 4 track. Access can be via Kirkby or the eastern section of the Outer Loop (old CLC line). HS2/HS3 trains would share Merseyrail tracks for a length from between Kirkby and Wigan to Kirkdale. Sections were 4 track and can be reinstated. The whole section used by HS2/HS3 could be 4 tracked by taking land besides the tracks and altering stations ensuring Merseyrail and high-speed rail do not use the same tracks. It can be accessed from the south using the Northern Line as dedicated HS2/HS3 access route. Tram-trains can operate from South Parkway down Aigburth Rd and the Dock Rd and get back to the Northern line around Leeds St just north of Exchange. A pedestrian tunnel can be cut from Exchange to Moorfields Wirral line platforms.
- Central: This site is near the shopping quarter. The line from Central to South Parkway does not run through any major centres, apart from Brunswick station. The lines runs through low population housing, and private housing estate, and is out of the way. The tunnel into Central was built for three tracks and is wide enough for HS2/HS3 two track. A tram-train can replace Merseyrail services running down Aigburth Road serving all the major centres ensuring greater takeup: Lark Lane, Aigburth Vale, Garston, Dingle, etc. It could run down Parliament St and onto the Dock Rd and branch into the docks and up the Wapping tunnel and into underground Central (engineering tunnel works would be needed) and onto the north of the city maintaining the north-south crossrail. The tram-trains could branch up the Waterloo tunnel to serve the Royal hospital and onwards to Edge Hill. It could also branch off at Aigburth Vale and run to the Dock Road serving the old Brunswick station and onto the Pier Head. Central station would be vastly expanded of course for the metro and HS2/HS3. A travelator can be cut to Lime St station connecting the two stations (which is needed right now). Southport and Ormskirk 6 car commuter trains can be terminated at Central. HS2/HS3 will have connection all over the Liverpool City Region.
Nos 1 and 3, means Central and Lime St are merged. Nos 2 and 3 means we have tram-trains that serve major centres better than Merseyrail. For some inexplicable reason Liverpool never builds local centres around metro train stations as all other cities do. Many people in Liverpool have never even been on Merseyrail. A girl I know in London was at Liverpool uni for 4 years, living near Bold St (near Central station) and never knew Liverpool had an underground metro. She would regularly travel to Aigburth by bus not knowing a fast metro line was there. This asset is poorly promoted and ignored by planners.
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If a concreter flyover enhances Manchester is doesn't say much for the city.

Few want to live in a city in which the car dominates either. The most attractive cities are those that are designed for people not cars. Underground metros hidden from view and do interfere with the surface, can provide the transport.