Yes, that’s exactly what Dark Samus is.
This isn’t the first time that Samus has had to fight her doppelganger: there was the SA-X in Metroid Fusion. Retro Studios once again used Nintendo’s first-party Metroid games as source material, and now we have a recurring foe for Samus to encounter. However, unlike the SA-X, it’s not declared as too powerful to fight. We just can’t beat it permanently.
And at last, we get into the more exotic parts of Metroid Prime 2! The stuff we find in this game wasn’t made by the Chozo, and so we don’t have classic elements like electricity, ice and fire to work with. Rather, it follows the general setup of light and darkness that the entire game revolves around. Similarly, our suit upgrades and visors won’t be classics. The general setup is mostly the same as the first game, but the particulars are quite different, and I like it a lot.