Boston-Spalding could be rebuilt adjacent to the original alignment, with some extra work to get the line back into Spalding & Boston town centres.
And agreed, though not always the case. E.g. reopening Garforth-Castleford would allow opening of new stations in East leeds, with services running all stops to Castleford via Garforth & Kippax.
Peterborough-Northampton, however, I'd want reopened with wires, and served by an LM Euston-Peterborough service, which could call only northampton, Wellinborough, Higham Ferrers, Thrapston and Oundle.
I think you're missing the point of what ATOC are looking at - they're focussing on areas which aren't part of the rail network and would gain real benefit form being linked up.
Spalding - Boston is no point, because both are currently on the network.
Peterboro - Northampton makes little sense either. There is a very good bus link between Northampton & Peterboro which is rarely full. Northampton, Peterborough and Wellingborough already have a good service. Higham Ferrers is close enough to Wellingborough to not warrant a station. Thrapston is close enough to Kettering. And also large parts of the formation are no longer available
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Well, it would make sense to have a few, just as the East-West line is considering multiple routes.
Why not:
Witham - Stansted, mostly following the Dunmow line.
Hertford East - Luton - Dunstable - Leighton Buzzard
Hatfield - St Albans Abbey
(and this, of course, on top of the existing East-West proposals)
Some great airport and parkway connections to be had there, as well as joining some dots and bringing back trains to some overlooked destinations (Dunstable in particular). Just get in quick before yet another (mis)guided busway is installed...
Braintree - Stansted makes sense and the route is largely available.
With Hertford - Luton - Dunstable, if you're thinking of reinstating the old Hertford - WGC and WGC - Luton that's a non starter. I don't think the Hertford E - Hertford N formation is available any longer. Hertford - WGC is available, but given that line closed years before Beeching it shows that it really wasn't viable.
WGC - Luton, the formation has been built on in WGC, the A1(M) was built after the railway had gone so there would be a very expensive crossing there, from Ayot - Wheathampstead various bridges have gone, Wheathampstead has part of the formation built on, and in Luton much of the formation has gone. Additionally, the only place you'd add back onto the network is Wheathampstead, which really couldn't justify a station.
Alternative would be a new line from Stevenage - Luton, but that would be straight across green belt land which is, quite rightly, protected.
Luton - Dunstable is becoming a busway. And from Dunstable - Leighton Buzzard the formation has gone, built on in Dunstable, Stanbridge and Leighton Buzzard.
Hatfield - St Albans is also a non-starter. Again, it closed years before Beeching so its viability is in doubt. Also the formation has been built on in Hatfield - I'm pretty sure the Galleria is partly on the formation.....
The only way you'd do Hatfield - St Albans now would be a branch off around Welham Green and through Colney Heath area - again all Green Belt and rightly protected.