In my view the decision to put the Hudson Line Access on backburner was about money, the much smaller political clout of the Hudson Line Riders, the LIRR's insistence on converting the Atlantic Branch to a shuttle and a little bit about NJT/ARC/Christie.
The details will never be known for certain as in who and when took what decisions, but with the MTA persistently short on capital funds and the politicos in Albany not willing to shell out much, when something had to be cut, the one that had less political power and the lower prospective ridership got axed. it was not necessarily the more expensive option that got cut as I have been trying to point out. Politically this might even be the correct decision because even if the New Haven Line Access is delayed and over budget if it gains its projected ridership it will make the case for the Hudson Line access to be implemented too. Going the other way around and building the Hudson Line access first and hoping that it turns out to be an enormous success and then being able to justify the New Haven Line access is certainly riskier proposition.
The other big problem that nobody brought so far is time slots into Penn and the platforms there. This is the one thing that even Cuomo cannot steamroll. If there are not enough timeslots then you cannot do the Hudson Line access. In all likelyhood, once ESA opens there will be enough timeslots for only one of the lines, either the New Haven Line or the Hudson Line, but not both. And if that is the case, then the New Haven Line is clearly the one that should get them. The main reasons why there will not be enough slots into Penn are two. First, the LIRR is converting the Atlantic Branch to a shuttle, so all the trains that currently go to Brooklyn need to end somewhere else and that somewhere else is the ESA and Penn reducing the total slots that LIRR can free up. Second, the cancellation of the ARC and its deep cavern left NJT dependent on Penn as a terminal for at least the next half century, so NJT cannot reduce its number of timeslots in Penn the way it would have with ARC. That reduction would have been small, but meaningful.
If there are not enough timeslots at the platform at Penn for the Hudson Line, the only solution will be Penn South. I personally do not see Penn South ever happening, but Hudson Line access to Penn might give a stake for NYState in Penn South that would have otherwise being missing and eventually give that project a push a few decades from now. It is just too bad that by then I would have been pleasantly resting six feet under for a long time and won't see it.