Bowen had a good idea posted on the facebook, and that is to just make the L2 scoring pick up where L1 scoring left off. I do think L2 shots should ultimately be worth more as you advance since there are generally fewer lit shots to hit. But the starting value based on L1 makes sense.
Others have mentioned using the Away Team shot in L2 and L3 modes, and I would agree but we don't necessarily need more Galactic Modes, although maybe some could still have them. Maybe it could also be used for a time extender or add-a-shot. I keep pushing for add-a-shot because that's one of the best features of STTNG in Q's Mission. They could also do it with the BH target, really useful for L3 modes that require do-over if you fail.
Something else that would be really lucrative for L1 modes is that that combo shots should add more to the base shot value, and the amount is directly tied to how the size of the combo string. Right now the base value increases by the same amount for each made shot. But what if your 2nd combo added 2x the value, the 3rd added 3x, etc. Similarly, the Warp Ramp combo shouldn't max out at 1M, keep it going, 1.1M, 1.3M, 1.6M, 2M (adding 100K, 200K, 300K to the base value based on number of combos). I also keep requesting that something in the game increase the base value of the multiball jackpots, 'cause I love them STTNG rules that do that with your left cannon shot and your pop bumpers. This would be a great Warp award, every 3rd or 4th Warp bumps the base jackpot value. Mmmmm, tasty.