I think JD doesn't seem deep because all the modes are timed and non-stackable, and there are no non-timed goals apart from crime scenes and ball locks.
You're right, though, it's easy to discount Supergame which has four multiball modes. How many games have seven possible multiball modes!? Blackout, Regular MB, Ultimate Challenge, 4 Supergames.
I think the depth is in how you choose to progress through the modes. With two shots that start modes (instead of a single shot like JP's Control Room) there is strategy in picking the best modes for the currently-lit mode start shot.
For example Pursuit is best started from the Sniper Tower because it feeds to the left flipper for a quick shot to the right ramp. If you make it quickly enough then you'll blow up the car in one shot. Or Manhunt is best started from the left ramp.
Then there is strategy in picking the best opportunity for that risky 2x bonus shot. And ensuring you keep as many crime scenes lit as possible to earn fortuitous EBs.