Ok, I've been checking the prototype out. Current findings:
*Spotlights in the first level are static.
*Zero has no music of his own.
*Different sprite for captured X.
*No miniature previews of each stage on the selection screen.
*Different snow effect in Blizzard Buffalo's stage.
*X will fall to his knees, hurt, when hit by Blizzard Buffalo's charging attack. This doesn't happen in the final version. In fact, this "hurt" animation also plays if hit by the body of certain enemies, like the two legged missile launchers. It's annoying, it makes you vulnerable and stops the game for a few seconds.
*Graphical glitches on Buffalo's ice attacks.
*The Doppler logo in the Maverick's life bar is slightly different.
*X's picture doesn't change color during the "Weapon get" screen. Also, there is no demostration of the weapon. The wireframe of the weapon is white instead of green like in the final version.
*No password screens after beating the bosses.
*Toxic waste lacks transparency on Toxic Seahorse's stage.
*Minor stage graphic differences, for example ladders in Toxic Seahorse' stage.
*Zero's death lacks sound effect.
*There is no miniboss in Toxic Seahorse's stage! The room is not yet there.
*Different background elements in Tunnel Rhino's stage (Large pipes). Background is different in general. Better on the prototype, IMO.
*Extra background elements in the beginning of Tunnel Rhino's stage. Spikes also look different, as does the platform where the Heart Upgrade is.
*Bit's homing's fireball is faster.
*Tunnel Rhino's miniboss wheels lack animations.
*Tunnel Rhino won't knock you off the wall if he charges into it.
*Fought Tunnel Rhino several times. Not once he used his drills. He just charged back and forth.
*Volt Catfish's sprites are entirely different.
*Different background in Gravity Beetle's stage.
*Gravity Beetle's giant blackhole will not always be spawned at the screen's center, it can also completely devour the top of the walls, which makes the fight harder.
*Vile's first Ride Armor is blue instead of gray like in the final game. It also lacks sound effects.
*Vile's sprite after he gets ejected from the Ride Armor is different. It then immediately switches to his final version sprite.
*Vile stops in mid air to throw his fire bomb attack.
*The polygon ninja star enemy on Blast Hornet's stage looks entirely different. More like a wheel with spikes. It's also WAY easier, being destroyed with 3 charge shots.
*Byte's sprites are entirely different. Also his magnetic mine is nowhere near as effective as in the final game.
*Two entrance doors to Blast Hornet's room.
*You don't stop dead on your tracks during the 'cutscene' with the enemy dropping from the sky and breaking the floor in Crush Crawfish's stage.
*No dash jump for Ride Armors! D:
*Some nice little extra graphics for Crawfish when he's electrified.
*The usage of Sub Tanks is glitched in the weapons menu. It works, but the graphics don't reflect it.
*Crawfish's boss room is larger.
*The Mega Buster with the improven arm cannon is glitched. If you fire a charged shot, X will remain in "charged status". You can continue to fire normal bullets, but you cannot charge. You have to switch to a weapon and then back to fix it.
*Different backgrounds for the second half of Neon Tiger's stage.
*Entirely different sprites for Neon Tiger.
*The helmet part's radar detects more than upgrades. It also marks mini boss and boss rooms. However it doesn't show missing items on each stage on the stage select screen.
*The Doppler lab re-emerges from the ground in the stage select screen every time you return to it once unlocked, instead of staying there like in the final version.
*The Light Capsule that gives you the Golden Armor in Doppler Stage 1 is blue instead of pink. The armor is black, instead of gold. Seems like a glitched sprite. If you go to the pause menu and back, the armor's colors go back to being the same as the normal improved armor.
*I got locked out of switching my weapons with the trigger buttons every time I got a new armor upgrade. Pausing and unpausing fixes this.
*I defeated Bit and Byte in the Maverick levels, which means the first boss in the Doppler level should be the garbage disposer thing. Nope. The boss room is still as if I hadn't defeated Bit and Byte, but if you enter, there is no boss, the level ends immediately. It seems the garbage disposer boss hadn't been created yet.
*ENTIRELY different background for Doppler Stage 2. Water is glitched, it was not visible until I paused and unpaused.