Seduction was originally meant to have two different Mini Bosses, SOD and GOM and Sidewounder. Due to time constraints, SOD and GOM and Sidwounder were taken out entirely, and the miniboss became Bio-Cardiac (but you fought its tentacles and not the main part).
Blazing Bomber and Rage Roader were taken out of Fury, also due to time constraints. As such, Crabburn ascended from Mini-Boss to full-fledged boss status. (The miniboss of the level was a weird vehicle thing with a wrecking ball)
The entirety of Spite except for the boss had to be taken out due to time constraints. It would have featured Greenhell (an evil tree), Cyburn (a dragon in a Shout-Out to the Mecha Dragon from Mega Man 2), and the Defiance Leader as minibosses.
Self was also taken out except for the boss. A large ship (Holy Ship) was supposed to be part of the entire stage. It was later retconned where Xero-Fin was supposed to be able to summon it. Alas, time constraints made it such that Holy Ship never appeared in the game.