Well, to be fair, neither Metroid Prime nor Fallout 3 are shooters; Metroid Prime is an action-adventure game, while Fallout is a (fucking amazing) RPG. They both just happen to be played from a first-person perspective.
Exploration has always been core to the Metroid games; aside from "weapon gates", wherein you needed a certain piece of equipment (example, the varia suit for most of Norfair and the gravity suit for most of Meridia) to get somewhere, you can tackle most any area in any order.
The same goes for the Fallout games. In Fallout 2, you were SUPPOSED to do a whole bunch of shit first, before discovering and exploring the Navarro Enclave base. But veteran players (or newbies who just had to read a guide) can quite easily zip on down to Navarro fresh out of Arroyo, pick up their Advanced Power Armor and Super Sledgehammer, do the Brotherhood of Steel quest (assuming you stopped by San Francisco first), and then collect your Pulse Rifle - you could have the best weapon in the game and second-best armor 30 minutes in, if you wanted. In both Fallout games, you could be picking fights with Deathclaws before Lv.6 (aim for the eyes!)
Both Metroid and Fallout games were big on exploration and discovery, so I don't think it's really fair to compare them to Half-Life - it's comparing apples to potatoes.
