The first one just had Meta Ridley guarding it, but this one has an even bigger construct.
Mogenar is our first true boss, and it shows. It requires fast action to prevent the boss from healing, but otherwise isn’t that difficult. One thing about bosses, particularly in Prime 3: since your health is your ammo, they’ll always be sure to drop lots of health. After all, you can’t have the player lose just because they don’t have enough health to damage the boss. That’s not saying I didn’t cut it mighty close at times, but it’s not like I was ever totally out with no way to get any more. Metroid has always made a way to damage bosses even when low on ammo (for example, Charge Beam traditionally damages bosses only weak to missiles), and this game is no different.
And at the end of the fight, Samus gets a little more corrupted. It has zero gameplay effects, thankfully, but it puts a worrying timer on her plot-wise. There’s actually a cut bit of dialogue from the game, where the AU says to Samus that if she lets the corruption get to her, she’ll become Dark Samus. And that’s what the full corruption cutscene shows. (You kind of have to let it happen to view this. Hypermode prevents most damage—thereby preventing most things that would keep you from firing—and it’s not terribly hard to mash A to prevent this problem.) None of the others have quite so visible a change, but also, Dark Samus got her form from Samus. It makes sense that there would be a bit more to it in Samus’s case.