It's been a long time since I've actively played on a mode other than Lunatic, so I can't really provide my views on how cards tend to be ordered there in terms of difficulty. But ZUN's "balance" in general throughout the series has been far from perfect, honestly. I don't know much about how ZUN codes the amount and speed of bullets to be fired across each difficulty, i.e., if the games use something akin to a rank multiplier or if he pays more attention to individual attacks than that. However they're coded, it still ends up causing some weird jumps in difficulty from pretty much any perspective, not just with a boss' attacks. There are many instances of a stage other than Stage 6 being the hardest in the game. Sometimes the difficulty will go down midway through the game before going back up again. As the OP alluded to, a boss' attacks often fluctuate in difficulty, sometimes wildly. But there are also instances of attacks either becoming easier or otherwise not changing in terms of "function" on higher difficulties, sometimes because the bullets are moving faster (sticking with MoF, Source of Rains is a good example). It's not something I think there's a real pattern to, it's just how ZUN wanted the progression of the game to go in terms of the styles of the characters or environment, but the general unevenness of things does become noticeable after a while.