The seats are better on NJ Transit, but I never had to take it as a commuting platform (only on the weekends into NYC or to EWR), but I found Caltrain to be so unreliable as to make driving 40 minutes up I280 to a BART station to be a better option.

Also their ticketing is messed up unless you're a regular with a clipper card, and even then it's easy to forget to sign on / off.

Not sure if trolling. I use NJTransit on a daily 2 hour commute. The main problem with NJTransit is that the ride home is almost never on time. 90% of the time, it's 5-10 mins late. But I can count on one hand how many times the morning ride has been delayed over the past 2 years, most of which had to do with atrocious winter weather affecting all the trains. If Caltrain had to deal with Northeast winter weather it would be 10x worse than NJT.