If you want to do a more Metroid-exclusive kind of game (not like a crossover), you should make one where you start deep inside a planet. Like in some underwater research lab, an entire "area" like that. You wake up without any knowledge of what's going on, go through the loops to unlock parts of the lab and escape into some deep terranian caverns. You'll find some "settlement" areas now and then, lab-like buildings, and as you explore more, you uncover more of the world you seem to be existing in. This is the inverse of the average Metroid game, where you leave a society and delve into a shadowy planet--here, you're in that shadowy place, and you don't have the solace of knowing <i>why</i>.