It depends on how you define deep. JP is about as far from deep as I can think of with a game - the main goal is to hit the shots during multiball for HUGE multiball jackpots. If you can pull that off, you get giant points. The modes are cool, but not necessary for the biggest points.

If it is just "stuff to do", TFTC is a similar era DE title that has more modes on it to do.

Having said that, I think JP is a better game. What it seems like you're looking for is more of a mode-based playing game, in which case JP will fit the bill just fine. I'd argue (although some people may laugh at this) that SF2 is a "deeper" game just based on the different things you have to do to advance, but I would definitely suggest JP before it.

If you are looking at something else, try the other DE DMD era titles, as they are all rather similar, but all have a bunch of modes to do - excepting LW3.