Some thoughts in no particular order...
negative thoughts-
I think there is potential for this to be a success, but the likely scenario is it will be a novelty that eventually wears off. Look at Syracuse OnTrak for upstate failed commuter service.
The vast majority of those that can afford to regularly commute by rail live in the sprawling suburban wasteland that stretches around the tri-city area, not close enough to the corridor to lure consistent riders.
The idea of bike-rail-bike or bus-rail-bus to go door to door may be exciting for the first few trips, but I think eventually the regular commuters would fall back into automobiles.
Albany/Schenectady doesn't suffer from highway gridlock, and even with city traffic, a door to door trip between ALB and SDY is likely to be similar in a car compared to a train.
The millennial demographic attending college in the cities will likely contribute to a fair share of the ridership, but not enough alone to justify the service.
if it gets off the ground-
a SUNY/Crossgates/87 & 90 Park-and-Ride stop is an absolute must.
a South Schenectady stop at the 890/Rt7 junction probably has some potential.
it would be cool if an Albany proper stop was feasible, but the NYC main skirts around the city and doesn't really duck through much of anything. Rensselaer it must be.
troy...
I'd really like to see Troy get service but the investment commitment for almost no guaranteed success (at least the Water Level Route already has 110mph double track and two stations), puts it dead in the water. Even if they were to pursue it, the South Troy Industrial is in deplorable shape, and even if you could get to the very northern end of it, you're still landing outside the city center, RPI, and Russel Sage. Maybe a 787 park and ride/intermodal terminal off the Colonie Main, or the stub of the Troy & Schenectady by Green Island, could gather some more downtown Troy ridership, but in addition to upgrades on the CP they'd have to completely reconfigure the D&H/NYC junction in ALB... Or bite the back up move on the connecter... no.
let's be optimistic-
The only way this service will succeed is if they develop good enough multimodal hubs to run the trains to and through. Rensselaer is good, and Schenectady is okay/needs improvement. A SUNY/Crossgates/Albany International Airport stop will succeed if you can get frequent enough bus service to all those locations as well as some of the suburban sprawl surrounding it.
Lastly, if someone else is willing to pay exorbitant amounts of money for it... Upgrade the South Troy Industrial, bust through downtown Troy to a new Green Island bridge. Follow the Colonie Main to Mechanicville, before swinging down to SDY on the D&H, and back to ALB on the NYC.
Did we ever hear a music sweeter than the one that thrills, as it floats along the Deerfield, as it echoes o'er the hills.
How we watch that little engine as it stalks across the plain; was there ever music sweeter, was there ever sight completer, than the coming of the train?
-E. A. Fitch