NYC/GCT has never really been a Waterbury branch priority, at least not in years. The biggest service priority was Stamford service, I believe. Again, intrastate should be the priority here, no one is talking about GCT service for Waterbury branch.
I can't recall on the fleet RFP for CTDOT, but were they considering DMU's, i.e. Stadlers? Perhaps that's the reason that they're not ready to go to bonding on those 12. As for the number, 12 would seem to me to be more than sufficient for the branch; it's the reliability and service level holding the branch back. Running three-car mini-bombs currently, that's 4 sets for twelve cars. I'd be willing to venture that only one car runs open anyway. 12 DMU's could run as six sets, which I would venture would be enough for increased service not accounting for any extensions. You could throw a couple sets over to Danbury as well. As noted, right now it's getting the passing sidings online, and increased reliability. Which definitely includes both power and coaches.
So to make short story long, it is disappointing, but perhaps it's to fine tune the request.
Next stop, Willoughby
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