The home world of the X virus is the home world of the metroids, SR-388. Moreover, as Fusion established, with Samus wiping out the Metroids on SR-388, it allowed the X virus to flourish as the Metroids were the primary hunters of that X species.
World-hopping was done in Metroid Prime 3: Corruption including going to the pirate homeworld. That said, they probably had to find a new base after the end of that game. I applaud Retro's efforts in making each world look unique and different not only from each other but also from the previous Metroid games. I also think they did that concept about as well as it could be done. In the end, I don't think it is worthwhile. I much prefer having a one large map planet adventure, than multiple smaller map worlds. Plus, to backtrack things were slowed down. Before, you just had to get on an elevator and to transport. World-hopping meant going to your ship, loading up the map screen, selecting the map of where you want to go and then the animation of leaving the world, travelling through space, arriving at the new world and finally you were off.
I'd argue that Fusion could even be considered an idea of this multiple world hopping idea. For most of the game, each space section you enter is its own world and you have to navigate and explore through it. Only at the end of the game, with the screw attack upgrade, are you finally able to start busting through these worlds and bring them further together abit. Even then, it can still take awhile to get from one section to another depending on where you are and how it is connected.
I prefer the pace of a one world game. Metroid Zero Mission really set the bar high for that.