I don't think my score is "so low" really. Try beating it, it's not as easy as you are assuming.
I broke my medal chain a few times, and had low medals throughout most of stage 6. The best run I had in that regard was with Midi & Meidi - I kept the chain up all through stage 6 and 7 in that run.
After you trigger the infinite lives, the rank is very high - much higher than anything in your runs! One death in a stage and you're in big trouble, in regard to score, as you have to revert to bombing for a bit until you can power up your shot again. And of course, while you're dying, you're also missing a lot of points. It really kills my score for stage 4 and 5.
You also have to get lucky on the stage6 boss. I didn't in this run (only one lightning blast two times). In my Kasumi ALL I got really lucky - 6 lightning blasts two times. Gave me nearly 2 mil on the boss fight alone.
I don't remember my scores after each stage in this last Lace run (I think I ended stage 3 with 4.6mil), but on a good run I get (w/ Lace):
st1: 900,000
st2: 3,000,000
St3: 5,000,000
After that it falls apart. I usually enter stage 6 with 6~6.5mil, get 3-5mil there, then 1-2mil in stage 7.
My best scores are definitely:
1)Midi & Meidi
2)Kasumi
3)Lace
4)Shasta
I'm proud of 1), somewhat happy with 2) and 3), and 4) really sucks. I really need to work on that last one.