In no particular order, here's a long post that I'm not sure who will even read:
IN's is somewhat interesting, but I wouldn't say it's the best.
MoF's is fun since you don't have to do that much to score. However, that also makes watching the world records not as interesting for the exact same reason. Also death = failure is annoying.
EoSD's is strange (bombing for canceled bullets?).
PCB's is fun but also confusing just because there's so much going on (instead of one main gimmick to focus on plus collecting point items at full value). And I'm not really a fan of the way unfocusing is nearly always better than focusing.
MS's is too simple (and heavily biased toward Mima), basically just survival plus collecting point items, though it's fun to get a score with letters in it.
LLS's seems to be primarily memorizing the best places to bomb for point items (which I never bothered learning).
SoEW's is luck-based depending on how many point items you can collect at maximum value.
HRtP's is somewhat interesting, but it's also the best way to play for survival, and trivializes the game more than TD.
SA I've never really tried scoring in, though graze auto-collect is fun.
UFO's is incredibly high-risk-high-reward. There's so many different ways things can go wrong, but when everything goes right, the points really start coming in... Probably my favorite to watch, but not my favorite to play (except maybe in Extra).
TD's is completely broken, and the result isn't even as fun as bombing through everything could be, since your resources are too strict.
In conclusion: I have no idea.
Also I second the vote for all the previous scoring systems at the same time (with adjustments so they all have some effect, and also limit the negatives like MoF's dying penalty and TD's bomb trivializing). As long as the limits are also removed, so it doesn't just max out at 999990 x 9.99 then crash when you summon a UFO.