The definition given in the rules is:
"a genre about cute girls having cute magical powers -- often associated with anime, manga, and other Japanese works. In my own personal opinions, some primary characteristics of the Magical Girl genre are:
1. Cute girl with magical powers.
2. Cute dresses -- not always though... some Magical Girls go the elegant route while others go the wild route
3. Transformation sequence -- not always but I think most do have it
4. Fighting against evil powers -- be it witches, aliens, or whatever"
Cute Girl: Check
Cute Dress: "not always though"
Transformation Sequence: Check
Fight against evil powers: Ridley killed her parents in front of her on eyes when she was 3, doesn't get much more evil then that. Check many times over
and finally, the big one:
Magic Powers
Part of the definition of Magic Powers Given is:
"A power the author may declare as not magical (e.g. machines), but mimics something you may expect if it were magical. To fit into this definition, try to replace the supposed "non-magical explanation" with "magic" and see if it makes sense."
She has much more athleticism then your average human (From Chozo DNA), immunity to X Parasites (The generic monsters) (from Metroid DNA), and laser beams (From her suit)
consider this sentence "Through her magic powers she has much more athleticism then your average human, has immunity to The generic monsters and can shoot Laser beams." That would make sense
Magical Powers: Check
Samus Aran, is a Magical Girl