As a preface, and I should hope this is unecessary given my track record, I'm not saying the bosses are too hard, but that most of the aspects that make them hard are for the wrong reason. Let's go over them. Try to imagine all of these bosses from the perspective of someone who is using the default gear that the game never tells you not to use and actively encourages you to craft. No Blitz Needles, no Magnuses, not even Brandishes. Leviathan Blade, Valiance, and Nitronome.

Snarbolax
I'm skipping that one sprite boss because whatever who cares.

Snarbolax doesnt have a single fun element to him. You pray to RNGesus that he's close to the bell and the lag isn't messing with you so badly that he'll be close enough to the bell to be affected when you hit him. What can you do when he buries under the ground? Nothing. How many times will he bury under the ground? As many times as the RNG says he will. If it wasn't for his gear, the game would be better off without him.

How it can be fixed
First off, the RNG should be removed. After 1-2 digs Snarbolax should be guaranteed to start biting. Furthermore, the bell should be more effective. When struck, the area should last for as long as its sound effect, so Snarbolax can enter the radius and get stunned a little after the strike itself.

Furthermore, the dig should be skippable entirely by hitting Snarbolax during the dig. This would be most easily achievable with bombs and large swords. Gun projectiles wouldn't register, but something like the explosion at the end of blaster's charge would hit, same as breaking ice used to work.

It should be possible to stack catalyzer shots on Snarbolax while he's invulnerable.

Royal Jelly (What? Who?)
Currently the least broken boss. If poison prevented lichens from merging, the preceding level would act as a good tutorial on how to defeat him.

It should be possible to stack catalyzer shots on Royal Jelly while he's invulnerable.

Roarmulus Twins
The first phase is fine. If you don't bring meta gear and time the first phase exactly right so you can hit both twins in one go, you enter the awful phase where you're at the mercy of RNGesus again. The moving head can decided to fire only at the top and bottom for as many times as it wants. After you beat this phase it's usually a bit more lenient and if you're diligent you can maximise chances of one head strafing into a rocket.

It's impossible to harm roarmulus twins with shard bombs. I don't mean that as hyperbole, they literally cannot be damaged by any aspect of them.

How it can be fixed
Both heads should share a health pool and neither head should ever turn truly invincible.

Hitbox should be extended to a bit inside the platform so that shard bombs can hit them.

It should be possible to stack catalyzer shots on Roarmulus twins while they're invulnerable.

Lord Vanaduke
The opening cutscene is a frivolous waste of player time on repeated runs. Any strategy that doesn't involve as many blitz needles as possible is severely gimping yourself and considered a challenge run that will take 10-15 minutes rather than 3-5. Watering is moot, as blitz needles pierce straight through, and if you seriously consider entering melee range you have to maintain the status of 8 fireballs in your head and when they're going to instantly reappear and kill you. Vanaduke can trap you in a corner with no escape, and so can fire tiles and deadnaughts. The mask is incredibly bugged, and if you water it while it's already watered you'll screw your party over. What should be a brief break in the main fight is a much tougher challenge than the boss itself.

How it can be fixed
The cutscene can be removed; nobody cares, ever cared, or ever will care. But if you must keep it, implement a cutscene-skipping mechanic where cutscenes are bypassed if all party members vote for it.

Fireballs should spend at least 5 seconds blinking progressively into existence before being harmful. Each removed fireball would temporarily nerf Vanaduke's normal defense specifically by somewhere around 30.

His piercing and shadow defense should be increased while his health is lowered. Vanaduke should be officially classified undead, and vs undead bonuses would have effect on him.

The complete immunity to shadow in the last phase should be removed.

Fire tiles should spend at least 5 seconds blinking into existence. They would disappear upon hitting a knight.

It should be possible to re-water a watered mask. Just getting the first water in should be good enough. For darkfire Vana, re-watering would not work, but would still not re-trigger the timer.

It should be possible to stack catalyzer shots on Vanaduke and his mask while they're invulnerable.

Battlepods
It's almost impossible to land hits on the battlepods with shards. Especially the ones Seerus have. Most battlepods you can't control when they shield and just have to wait for a really long time before getting a short window to do damage. Waiting is not a good game mechanic.

How it can be fixed
Hitbox for battlepods should be considerably more lenient. Downtime for the shield should be longer to accomodate bombs and other weapons that aren't blitz needle, but would be damage-gated and spring back up after too much damage. Health should be lowered.

It should be possible to stack catalyzer shots on battlepods while they're invulnerable.