These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Among the generic bosses, Clock Trap is a order of difficulty much higher than its compatriots.
And of course, everyone else who can make a decent boss is less then one step away from such a title!
What Do You Mean, It's Not Symbolic?: Several bosses are re-imaginings of deities from several religions (Eboshidori's guardian series is built around this, with every Buddhist Deity except for the Buddha himself showing up and the protagonist being the Buddhist devil ), one sticks the player on a crucifix, and one crucifies himself to achieve his final form.
Arc Legion: "You still cannot give in to the inevitable? Then let the heavens fall!"
Designated Hero: Mara. No matter who created him or why, no matter the intentions, Mara has the simple mission of killing Sakra-Devanam and her spawn for attempted (and possibly accomplished) genocide of humanity. If he needs to devastate an alien fleet for making the simple mistake of experementing with Sakra-devanam's oddly shapedressurection leeches, so be it.
Nightmare Fuel: Eboshidori's storyline: shortly after Mara's fight with the Phantom 30k, he destroys it while the pilot is calling for backup.SET TO CREEPY MUSIC. It's implied that the P30k and all related ships were created by Sakra-Devanam, and are not human, but still....