The regular game's scoring system is fun too, though I think there are some nuances I haven't really understood yet - so far I'm just playing it as 'get as many 5s as possible', which while useful might not be all there is to it since I seem to be getting pretty low scores in comparison to my distance (my highest for a 1-all is 70m so far).
Well, the system is actually very simple. The whole ST thread on shmups.com can be summarized in a few brief sentences.
? Killing stuff with normal shot releases chips depending on distance from the target. It doesn't decrease stage multiplier.
? Killing stuff with lock-shot releases more chips from enemies but cashes the multiplier in
unless done in a chain.
? Picking up a chip starts a chain, during which
every destroyed enemy releases chips of the same value.
Thus, the whole scoring system is about taking out a single enemy and plowing through the rest with lock-shot for a couple seconds. Rinse and repeat. There are several keys to making the process more efficient, which I arranged in order of importance.
1. Make sure not to cash in your stage multiplier on something that isn't worth it. Midbosses (main bodies, not the parts!) are always good. Large enemies near the end of the stage are also good; consult the booklet for their exact point value. Destructible (mid-)boss parts are
VERY BAD; only destroy those for chips or leave them be if you can't.
2. Build longer chains, as killing stuff with lock-shot releases way more chips.
3. Spare lives and bombs are factored in at the end-of-stage score tally, so don't die, don't bomb, and get the secret 1-ups if you can. It's not a whole lot, but it's significant: about 15?25% of your first loop score comes from end-of-stage bonus, with a maximum of about 65 million, or something like that (SPS gets 62 in his 512 million run, which he has since improved by 47 million). Survival obviously takes precedence, though.
4. Master the empty lock technique (easier with Panzer Jager since it has longer lock-on period) for more chips off unchainable enemies. Not terribly useful, but allows for receiving the first extend already on stage 1, among other things.
As you see, the system is really simple and largely intuitive, which is why I've been able to score and enjoy scoring right from the beginning.
Hope this helps!