Quoted from shacklersrevenge:

I'll throw my thoughts into the debate, since I've owned both a few times and own STTNG now.
IJ theme is better than STTNG, it just is. IJ does an incredible job of sampling from the franchise and making you feel you're ''on an adventure'' and has one of the best, if not the best shots and super jackpots in all of pinball. The callouts are superb. When you smack that captive ball to get the whip crack for 100 million, does it get any better? There is a serious knock on IJ though imo, and that is it's way too easy to get multiball going, and it's right in your face to tempt you to do it. Great modes in IJ.
On the other side, STTNG is a definite Steve Ritchie masterpiece. I wouldn't have the outlanes any other way, and yes they can be frustrating and leave you one shot off a lot of times, but if you're on your game, you can pound STTNG to the moon, and if you're not, it will snake you all day out those outlanes and leave you well under a billion for a game.
The mutliball is more or less an afterthought in strategy because of how much else there is to do in STTNG, between the main modes and the neutral zone modes, when you do decide to go for multiball, it's perfectly executed and that shot into the Borg is also in the running for best shots in pinball, that is one fantastic Super Jackpot. The shots in general in Next Gen are better than in IJ imo. The extra flipper over IJ really gets a controllable flow going.
If you want to talk about great theme, really nice backglass, coolness with excellent gameplay, IJ is that game. If you want to talk about a masterpiece, with super flow and near perfect gameplay, STTNG is that game.
Both awesome games, and both have superb callouts and gameplay, but I feel STTNG edges it out overall.