Just looked that up and it said non-linear, interconnected world and the upgrades are useful in the world for travel and combat as well as being needed to advance. So I guess it does.
Shantae is frequently compared to Metroid; I haven't played it yet, but from what I've heard it follows the Metroid formula pretty closely, with some great twists that make it unique. I thought maybe you considered Shantae more 'Metroidvania' like you were talking about, but I guess you just hadn't heard much about it. :P
Anyway, I'd love for WayForward to tackle Metroid after they finish this Shantae game. If you're itching for some Metroid action on your 3DS ASAP, Risky's Revenge is available in the DSiWare section for a kinda-steep-but-probably-worth-it price of $12.