While playing through Mega Man Zero today I came to realize something...
The Mission Score system, more specifically Elf Usage, is bugged!
Here's what should have been default behavior:
Use Elf in mission or right before the mission, only the amount of elves used then will be counted. So if I use 2 elves in the previous mission, 3 before the current mission, and 1 in the current mission, it should count that I used 4 elves and give me the corresponding penalty.
However that is not happening! Instead, every elf used at any point is counted and gives a corresponding penalty while claiming you used no elves whatsoever. It can go so badly your post-mission Title can become "Buggy", and there are elves and content permanently lost due to this bug (requiring a fresh start to fix it)
So, here's some ideas on how to fix it between Z1, Z2 and Z3:
PLAN A: Elf stays in the Mission Status, but without the penalty at all, in this case serving only as an "extra info". This would involve increasing something else's value so 100 points should be possible in all missions.
PLAN B: Elf stays in the Mission Status, but only elves used during the mission are counted and gives its corresponding penalty. Any used outside the mission is out of the math. That would mean making it so each elf costs 5 points (since the max for no elf used in 2 is 15, that means using 3 would down that to 0)