I felt sort of dropped in an out of place area as the film began, I don't feel a good connection for the universe or anything in it, probably because the exposition was either poorly explained or just poor in general (no offense but I really have no grasp for why I should care and who these characters are).
I got as far as there's the mercenary sister of Goombario trying to protect the mushroom kingdom and her friends. Oh and they Shy Guys are pissed for being mercenaries (which they can't change through reasonable means for some reason).
The music was fantastic and well executed and your show of effort was bleeding in the animation (you used a TON of great techniques). Your blend of animation really shows and it's interesting but on a personal scale I find it kind of like a collage and a bunch of scraps taped together, it's overall not that appealling and awkward. I'd rather have the whole thing drawn or sprited, not the two in one scene, the two styles in seperate scenes are okay though.
I also have to say your sprite work was full of notable effort, but I felt the protagonist's spritework especially with her goggles on looked plain bad and shoveled together (and I know it wasn't but it feels that way when I'm watching it). I think you have to work on your lip syncing and goggles in the drawn portions otherwise it looks great.
I kind of hate your protagonist and find her unrelatable, her flat "too cool for school, I got all the answers, bored as hell attitude" was somewhat pathetic and dull, especially since she reacted so poorly to any situation put in front of her (YOUR BROTHER/??? JUST GOT MUTATED AND YOU'RE ALL "so what?") and since she has no backstory I can establish as reasoning for such cool headedness I don't see how I can understand her as a character. Her voice actor was good but I feel she was a one-tone, emotioless voice all the way through making her sound incredibly generic. Your other voice actors were amazing at their parts (kudos to green shyguy and admiral).
Hope you continue and improve, good luck.