Both are great games and I currently have them sitting next to each other in my collection. I honestly love the gameplay of STTNG just a bit more. It has a great wizard mode that's very achievable and very satisfying. Plus, your performance in the modes working your way up to the final mode has a huge impact on how well you score in the wizard mode. I feel this machine is one of the best values under 5k.
Both machines have awesome call outs and theme implementation, But I like the theme of IJ better. It's also a super fun machine to shoot and I love the fast ramps and orbits. I still haven't made it to Indy's wizard mode since it seems like quite a feat to get thru all 12 modes (at least with my average at best skills). Also, IJ seems to sell for several thousand more than STTNG. Because of that, my vote goes for STTNG. Like many have said, both are great and It's hard to go wrong with either.