As someone who rode a lot between upstate and Manhattan both before and after the 1991 transfer from GCT to Penn, I can say that I really much preferred Grand Central for trips where New York City was the destination. For most of the past 30 years, of course, Penn Station was a dump, so GCT was just a much nicer terminal from which to arrive and depart, though the opening of the Moynihan train hall has really evened the score on that point.
One thing I really miss about Grand Central is that the trains were serviced underground in the terminal, which meant that, in foul winter weather, there were none of the delays associated with the Sunnyside yard. Trains were never "delayed en route to the station." Instead, they were ready on the platform with the gates open about 20 minutes before departure, which made the boarding process so much more relaxed than Penn's mad scramble for the escalators when tracks are announced a few minutes before departure. So, it just functioned better as a terminal.
And Grand Central was closer to the core of the Manhattan office zone, so for business travel, there was a much higher probability of being able to walk to one's final destination from there, whereas arriving at Penn was much more likely to require transferring to a subway or cab.
But of course, the great advantage of Penn is the ability to make connections. If you're traveling from upstate to Philadelphia, Washington, Virginia, Florida or anywhere else to the south, transferring at Penn is way easier than having to schlep one's luggage across town (and having to allow an extra 30 minutes to do it). And there was a considerable savings to Amtrak from consolidating into one New York station instead of having two. That's why the West Side connection was built, and why I supported it at the time. And once the connection opened, we got more service between Albany and New York, because being able to make connections more easily suddenly meant there were more riders.