I enjoy all JJP pins, just wanted to say that before you read below lol. I'm sure a good number of people will disagree with me.
As of today I would say The Hobbit is the best pin JJP has made to date. It's taken me a while to come to this conclusion and playing a lot of other modern pins. Yes the game doesn't have the best layout of all JJP pins but in my opinion it has by far the deepest level of theme integration ever created for a pin. Most mode based games are lucky to have a half dozen modes that feature the level of choreography (animations, video, music, sound effects, etc all timed to shots) that the book modes in The Hobbit contain. TH contains 30 main modes, the book modes, that not only feature great choreography but also excellent sound / music. Then there's the 3 Arkenstone modes that are deep with multiple stages.
There's also the toy / feature aspect of The Hobbit. It's beyond loaded. 11 drop targets, an interactive dragon toy that moves / talks, kickback, 4 molded beat pop ups, laser etched metal ramps, subway, two magnets, and a mini LCD toy all in a widebody pin, damn. All of those mechs are used in interesting ways thanks to the incredible code work by Keith Johnson, and Ted Estes. The sound design by David Thiel is among the best in pinball. Hell, there's also dozens of custom tracks in the game created by a Hollywood music group, Two Steps from Hell.
Pirates may have the better layout but the lack of licensed assets hurt the game deeply in my opinion and is why I sold it earlier this year. There's 125 main modes in Pirates but it might as well be 1 considering there's little mode choreography in them due to a lack of assets as well as only ever hearing one voice in the game. The pick a character feature mixes things up for the how modes are played / scored but its not the same as the deep objective based modes in The Hobbit. If Pirates had the same level of licensed assets as Hobbit it probably would have been my favorite pin.
My favorite pins are objective based, that tell a themes story through its code, and have a variety of modes with multiple levels / stages with great choreography. The Hobbit does that the best in my opinion.