The reverse S design was already considered and the Y network was still chosen, Underground through stations in every city would be copiously expensive as well.
Everything associated iwth HS2 is copiously expensive, and given that all of the cost estimates for HS2 (and thus scheme optimisations) were based on valuations of property etc that were entirely worthless, every output from the process must be considered poisoned.
I don't think the scheme, as envisaged, fits into the wider UK railway network well at all. Thanks to demand for fast services to continue to avoid "punishing" intermediate communities, it seems that there will be negligible reduction in operating costs on the classic lines that are "relieved", as well as few if any paths actually released for other uses.
And hub/out of town stations are fine, the countries with the best HSR networks, Japan, France and China use them extensively, Shin Osaka isn't even a central train station, and China uses Stations at Airports a lot.
Japan don't really use out of town stations in the way HS2 proposes though.
Given Japan's comparatively lax planning laws the out of town stations become in town stations rather rapidly.
That can't happen in this case because planning law will never allow that kind of massive development.
And in France the out of town stations are transparently a political sop with, in most cases, negligible actual transport value.
Neither option is particularly applicable in the UK context.
HS2 as designed was a perfectly fine scheme, not perfect, nothing ever is, but good enough. It was cancelled because the ruling party is in disarray, nothing more, nothing less.
I know it would be preferable if this was true, but the reality is the scheme was collapsing long before the political cuts started.
Even before they started axing things the NAO concluded the scheme was very much not going well.