The P3 in general for so many reasons (take your pick):
1) Commoditized, modular boardset: Driver boards and switch boards placed near the switches, coils, etc. to reduce wiring, each exactly the same as another to aid in troubleshooting, repair, and replacement. This is huge and not something that anyone else is doing (aside from those using the P3-ROC, like API).
2) Modular playfields: the back 1/3 is traditional wood and can be replaced easily to provide you with another game or games.
3) Multiple game launcher: first commercial pinball that loads multiple games on the same playfield without changing DIP switches or connectors.
4) LCD playfield: bottom 2/3 is LCD, allowing for dynamic information to be displayed at all times. Others have embedded screens as well, but Multimorphic has another trick up their sleeve --
5) Dynamic ball tracking: using some clever opto tricks, the ball is sensed at all times on the LCD screen, which allows for dynamic targets and really cool interaction between the LCD elements and the physical elements of the pinball machine. It's really neat to see the slings fire when a bug flies into them, for example, squishing the bug.
6) Service position: The playfield comes forward about 1/2 way towards the front of the cabinet and can stand completely on its end while you poke around to service. It's amazing.
7) Other service enhancements - solarvalue showed the flipper and sling mechs - they just slide out and are disconnected with a single connector. Pretty big deal. Every mech can slide out, and flipping that back 1/3 wooden playfield around to adjust pop sensitivity is trivially easy compared to any other game.
8 ) SDK for developing your own games: They are the first company to encourage homebrew or commercial development on their platform. This is really huge. I am developing a game, and I'm sure many others are as well. It's fast and easy to get started and is really straightforward. Uses an extremely popular game engine for the bulk of development with a ton of resources to get you up to speed. The pinball-specific stuff is very very similar to pyprocgame or skeletongame, if you have used either of those.
I'm sure there are dozens of other innovations I'm forgetting, but these are what come to mind for me right away.