The beginning of Metroid Prime started that way too.
She had a small number of her upgrades. A few missiles, the Morph Ball, Bombs, the Varia Suit, and the Grapple Beam, if I remember right.
This time, she has nearly all her power ups. She doesn't lose them in a fluke explosion or an Ing attack; rather, she chooses not to use them until Adam Malkovich authorizes it.