ST is all about combos. Practically any shot is doubled if hit as a combo. Also, the points you get from a mission can vary wildly. Obviously on lv 1 missions which are timed, you can just hit more shots in that time and hit more of them as combos (with increasing score for each shot hit, too). But take Prime Directive II as an example. You could just hit all 7 shots on their own and complete it. Or you could go for the special two-color blinking shot for 2x points (or combo to them for 4x). In theory I think you could basically do a whole playfield 7-shot combo for massive points.
You can combo the final shot to destroy the Vengeance for 10 M instead of 5 M. Combo jackpots in multiball are 2x. You can combo shots in Kobayashi Maru Multiball to get 2x the entire score you earned in one of your previously completed missions.
Warp ramp can get you an extra ball and it's also worth good points. If you have Super Ramps active, the value is double on the Warp ramp. So if your Super Ramps are worth, say, 1 M, a left orbit to Warp ramp combo shot will be 4 M.
Yes, the lv 1 missions aren't the best and the lv 2 and 3 are much more varied and fun. I hope they do something to make going 3 missions deep more rewarding so I don't just find myself playing lv missions the vast majority of the time. But have still been having a lot of fun with it so far.
You can't stack everything, but you can have a mission active along with a multiball, or something like Vengeance Scoring active in multiball.