Nice to see data informing choices.
Would action on Colwich be the same irrespective of HS2 'developments'?
Which, if any, would you consider a quick political win?? I sense Ely North has been 'warmed up' in political preparation, linking to East-West railand growth- rail-accessible housing in 'the arc' and Felixstowe Port exports.
Others could be 'mitigated' by longer, less frequent, trains with fewer conflicting moves, eg London 'suburbs', incl Basingstoke, Woking, and Selhurst, assuming more Working From Home meaning fewer commuters?
Easiest and cheapest win?
Probably Greenhill Upper. Although the benefits would be questionable for the cost. Law Junction, although again, questionable BCR.
In terms of actual benefit, the highest BCR would undoubtedly be Woking. It would be expensive, although not as expensive as one might imagine. You could do the whole thing in railway land, and you'd have to demolish a bridge, but the main cost would be the blockade you'd need to build the thing and reshuffle the track geometry.
Politically, the Selhurst Triangle is going to need to happen at some point. Capacity is limited at East Croydon station, and the whole scheme would cost an arm and a leg, but the benefits would be substantial. Think of all those juicy marginal constituencies in the London commuter belt.
Four tracking Wigston Jn to Syston Jn, including grade separation of the former, is already necessary for capacity, but doing so would be a very very visible investment in the Midlands.
I suspect South Kirkby Jn or Swinton Jn might need doing at some point, probably the former as it would be easier. Grade separation would allow you probably an extra path each hour, and combined with electrification from Fitzwilliam to Sheffield, would massively benefit South Yorkshire's rail network. Swinton Jn would be expensive, South Kirkby Jn cheaper, but you're still building a new bridge and new alignment over the ECML.
Remodeling Golbourne Jn to take the line over the WCML and connecting onto the slows would be great as a nice to have, politically very easy, and if you took the line as a possession for a month you could do it cheaply.