I'm still puzzling it out, actually. The trains and the little root/asparagus rockets are driving me crazy; it still seems completely random.
I did discover that you get the most points from destroying targets though (bigger points, bigger gems, bigger combo), so getting ridiculous scores is a combination of racking up kills in quick succession and using bombs at precisely the right time (peak multiplier), preferably around the target stations. The game's different endings are all definitely dependent on scoring, so getting to that peak multiplier is doubly important for progress. I managed over 2 million points once using a single bomb because I allowed myself to become surrounded and happened to have weakened one of the towers just enough to include it in a massive combo.
Some of the environmental damage also appears to be bomb-able, so while you can shoot the windmill or the weather vane for a few thousand points, you can wrap them up in one of your combos and score much, much higher by bombing it at the same time as a bunch of enemies.
Oh, and the game doesn't better reward either time or number of enemies killed: it weighs them together, and there seems to be a middle point that nets the biggest returns. So the more you kill in the shortest amount of time, the more points you score (of course), but don't do it too quick because you might miss out on environmental triggers or other things that happen within a set amount of time. It's nuts. The trick is, in part, planning a route so that you can trigger environmental damage, kill enemies, and take down targets in a way that prevents the combo meter from depleting. I tried several times to see whether or not I would get more out of staying on a level or chewing through it and found I was always getting better bonuses at the end of the stage when I balanced the two. I've also found that it helps to take every other target down and use the time in between to build up that combo meter. Theoretically you could wait to build up your meter complete before destroying a target, but I think it'd be hard to take down the targets and keep you meter high.
Anyway, I think people are still puzzling this thing out too. I have found virtually no help on the Internet and what I have found is in Japanese and not as helpful as I'd like it to be even when translated in what seems like a competent way.