Marie's different forms are weak to different things. Her first form is weak to projectile spam; the floating skulls move slow and get chewed out by other projectiles. Painwheel can spam Stinger (M) > Fly > Unfly (you can also bail out of charging the stinger early if you have to). Peacock can just go nuts with whatever, Parasoul, Robo Fortune, and Fukua can also be really passive aggressive. Valentine can actually poison her and wait her out, and play lame or chuck scalpels when you get the meter. Most other characters just have to power through it.
Her second form basically can't deal with the magical strategy of "Hit with your launcher, jump cancel forward, hit a button on the way down." Then do another launcher as soon as you land. Repeat as needed. Jump cancels are Super Jumps, so you'll turn around after you cross over. You don't have to worry about having a cross-up button. You can switch sides over and over, and you'll usually be really high in the air or trick her into attacking the wrong way. It's cheap, but Marie doesn't play fair either, so screw it. Don't feel bad; she deserves it.
The last phase is too dense to strategize much. You just kinda have to smack her as much as you can real fast to get the fight over with. Save as much meter as you can for this part, and blast her with your Level 3 if you can. Just use whatever you've got.
Lastly, there's Marie's kryptonite: Diamond Deflector. Precisely 100% of Marie's attacks can activate Cerebella's projectile counter, Bella is invincible to all of her attacks until she's able to move again, so you can counter again or just block against the bone dragons, and the counter projectile uniquely hits Marie every single frame it touches her. A single deflector will do about 10x more damage to her than it would to any other character, and you'll gain about half a bar of super meter for each deflection. Marie cannot block the counter fireball, cannot move out of the way to avoid it, and can't attack you with a move you can't counter.
Bella vs. Marie is actually an honest-to-God 10-0 matchup. Meaning it's literally just impossible for Bella to lose if she plays the matchup correctly, which she can do every single time. It's more of a tragic comedy than a final boss fight when you know that.