I *LOVE* JP the way it is, but I have had a few ideas every now and again...
The first is like you said, the doors for the gate would be cool to actually be molded, and as for them opening and closing, I think it would be neat to do that based on the diverter on the ramp -- when the diverter opens to return the ball to the left lane, close the doors. It should theoretically be possible (although is probably more work than I would ever care to do to install it) and would make it so that you are never shooting the closed doors.
The Control Room could have something sculpted to go above it that integrates the two lights and actually makes it look more like a control room. I've always thought it was odd how it is just the two lights above it. The bunker is less of a big deal, but could be the same way.
The boat dock shot in the back is screaming out to have something boat-dock-ish added to it.
The little metal box that says, "SHOOT T-REX WHEN LIT" would be way better to be either a stalled jeep from the movie, or something else. Maybe wired so that the light triggers the brake lights on the jeep. I once saw someone do a mod something like this with a small JP Matchbox car style toy, and it looked okay, but it still had the light sticking out the top and I didn't like that.
Finally, the thing that I feel like needs it more than anything, and the thing that I have honestly tried coming up with something for a couple times -- the Raptor Pit is one of the most intimidating shots in any game, and yet it isn't celebrated at all. I love the mounted Ram on BBH for the similar shot. I have tried unsuccessfully mounting a raptor toy back there (it looks like a raptor toy). Other ideas would be building up the sides of it in 3D just a little to make it actually look like the raptor pit, and / or even putting a little top on it with the trees or whatever. It has always bothered me that the game has something that celebrates pretty much every other shot except for the most dangerous one in the game... that has nothing. The stupid captive ball shot right next door has the amazing mosquito in amber... why doesn't the raptor pit have *something*?