Is the body text [of the Williams-Shapps Plan] in Rail? I doesn't look like it to me, but then I think Rail 2 comes in various different flavours and I don't know what they all look like.
Rail Alphabet 2 is used for text in Network Rail's design guidelines, and works very well, but in the Williams-Shapps Plan it's Helvetica Neue for text. Rail 2's signage and text 'flavours' look pretty similar to each other (I think the signage version has slightly narrower letters), but not terribly similar to the original Railway Alphabet: the numbers are the parts which match most closely.
While Railway Alphabet was completely neutral - and often indistinguishable from something like Helvetica without careful study - the new version is actually quite distinctive. It's quite a clever update that doesn't look too 'of the moment' or too '1965' either: it's definitely not just a revival of an old identity, just a return to the basic principles of signage design that work just as well today as they did in 1965.
We need a modern take on this and digging up corporate identities that have been dead for 25 years isn't the way forward
It's possible to reference old identities with a modern take: GWR and Southern for example, which had both been dead for a lot longer, were deliberate attempts to do just that in very different ways. I suspect the intention will be to do something that is reasonably up-to-date but fairly timeless, so that it has a chance of lasting at least as long as it takes to update everything. Mind you, given that it's only a few years since the supposedly 'permanent brands' of LNER, EMR etc have been introduced, nothing is certain. If InterCity returned, I'd expect it to be nothing more than a sub-brand to highlight inter-city services provided by each region, as it is on EMR, with a common minimum service standard.