My issue is that there often does not seem to be a higher level strategic overview of the rail system and the public transport system in general. Longer-term goals and targets, ideally with cross-party support need to be defined (e.g. a specific percentage of modal shift, reduction in miles driven, connectivity for XX thousand new homes, or targeted economic development of less developed regions) with measureable metrics. Then those high level goals can then be used as a baseline to develop local projects which can be evaluated based on how much they contribute to acheiving them. BCR is then a tool that can help evaluate which projects should be carried out first, but even then it should not be the only or the most important criterion.
Currently it seems to be that if these high level goals exist, then only in a dusty drawer of a civil servant's desk, and they get re-defined on a whim every time there is a change in government, at least in Westminster.
As two simple examples, setting a modal split (by trip) target of no more than 40% for car trips would likely lead to massive, much-needed investments in walking and cycling, large investiments to massively increase the attractiveness of rail transport in urbanised areas outside London, and ideally also a reevaluation of the approach to new housing development, strongly discouraging extremely car-centric housing estates with no amenities reachable without a car.
Setting a target for modal split by distance (rather than by trip) would see investments in high-speed intercity rail.
Officially adopting Vision Zero (zero road deaths) at a national level is likely to lead to significant investment in road safety programmes, and also on modal shift towards rail (fewer drivers = fewer deaths).
The challenge for BCR calculations, particularly in rail, is that planning horizons are too long for any purely economic calculations to be made with any level of accuracy. Of course if you pay some consultants enough they will come up with very precise numbers showing onw thing or another. As has been shown time and time again (Borders, Okehampton, etc), the reality often looks very different. New base tunnels have a design life of at least 100 years, meaning their economic impact is impossible to accurately predict. But it is still pretty obvious that the connectivity that a base tunnel could bring will still have economic benefits even after 100 years. The other issue is that the current BCR approach tends to only consider projects in isolation, and each project at-best poorly estimates its network effect on other projects or on the country as a whole.
It is inherently a political choice which targets to set at a national level, but once they have been, I strongly believe that the government should set a framework and then delegate the implementation, particularly of smaller projects, to local government, while also giving them more power to retain their own funding through local taxation. Westminster should not be deciding which areas get zero-emissions buses or whether a specific cycle lane on a specific road should be built. In that sense, like everything else, poor transport policy is a symptom of poor governance in general. Given the amount of scrutiny and evaluation HS2 went through, it should not have been possible for the PM to scrap it on a whim, with no democratic oversight whatsoever...