I think ST-TNG edges out Indy in features and is a better value for your dollar. I like the Indy theme better, the music from the movie gets you pumped up and excited to play it, the tighter playfield works with the game layout, more risk/reward with shot locations, as in, you miss a shot, it's back in your face faster.
Indy has Multi-ball, Modes, drop w/captive ball shot, Path of Adventure. ST-TNG you still have Multi-ball, Picaard/Warps, Modes, holodeck, cannons just to launch ball (but more just a toy). For ST-TNG, out of those options, it seems to have more balance and multiple ways out, I like games like that. 3 ramps (ST-TNG) vs 2 ramps Indy, not that it matters that much. Skill shot on ST-TNG lets you pick options as well, lane plunge for Indy. Both have weapons for triggers.
When I play both games on route, if something on a ST-TNG goes down, it's more enjoyable than if something on Indy isn't working.
Both are great games, if I had 5500-6k and didn't care, I'd probably pick Indy, if I wanted to spend 4500-5k, I'd pick-up a ST-TNG. Once I start getting near 5k, I start thinking new Stern (Pro-version) game.