I recently bought an LE and have no regrets. Having Gene Wilder adds to the art package, and the sparkle blue rails / wireforms are really nice looking. To me, physical Wonkavator makes it pretty rewarding to lock the ball and/or or to start Wonkavator multiball (or in some cases have it stolen from me). I think its great that the SE has virtual locks, keeping gameplay largely consistent across the SE and LE versions. (As an aside, does anyone know are the Wonkavator virtual locks displayed any differently on the SE's display vs the LE?)
If you go with the SE, I would definitely recommend you add a shaker motor. It's clear that JJP spent time getting the shaker effects right. They really add to the atmosphere of the game. Not jarring or startling at all - more of a smooth rumble that is well-integrated with different modes.
Good luck!