[hannasanarion]

That is true of all public transit systems, period. If you want to get from Bayonne to Yonkers, you're going to have to go through the central hub of Manhattan, just like if you want to get from Garching to Unterschleißheim, you're going to have to go through the central hub of Munich.

This is just the nature of public transit outside city centers: they will have a hub-and-spokes shape. That's because this shape suits the needs of pretty much everybody: travel from one spoke to another is way less common than travel to and from the center, and if you really need that route and can't afford the time of going through the hub, most metros cover the concentric routes it with lighter options (like two-digit NJTransit busses and the Hudson-Bergen light rail).

The corner cases of suburb-to-suburb trips and short distance vacations aren't important enough to necessitate complete infrastructure capitulation to drivers.

And for the vast majority of New Yorkers, a car isn't necessary. Car ownership is around 45% in New York City, and that number goes way down if you exclude Staten Island and the outer parts of Queens and Brooklyn that don't get subway service.