Slightly confused by your complaints r.e. jfk > manhattan via mass transit. You get on the LIRR and you end up in penn station. It's not the same as grand central but from a connectivity perspective it's similar. I've taken the train from Zurich airport to Zurich HB and while I recall it being fancier it's not like it's materially different (both go from point A to point B in a reasonable period of time at a reasonable cost).