Rockets make everything cooler. But some people just hate heels regardless. They exist solely for appearance so that we can ignore how uncomfortable and pointless they really are, even in the real world, so I don't really pay much attention to their practicality in games.
That's just that game and that's basically only that way because of the ability to recruit new characters. Otherwise it'd be the same as all the main series games (Which Powered up does not count in because of its status as the only game in an aborted remake series of the classic games.)
It could be just as easily argued that destroying a robot is merely for the sake of gameplay simplicity, though. In ZX, for example, Model A obtains data through victory, whether the opponent is killed or not.
The finer points of how Classic Mega Man absorbs weapons are something that each spinoff tackles individually (IE, Archie's comic follows the old RS route).
...I'd also point that the nature of Smash Bros. would have allowed absorption upon defeat as well, since a single-stock-one-on-one match is pretty rare.
And his relevance really just ends there until Super Metroid. Other than that he's a recurring boss. That's it. He's not THE antagonist because Metroid doesn't have a single antagonist that overarches the entire series. Any other villain in Smash is. Ganondorf is, Bowser is, and what do you know, they're the only antagonists in Smash. Wolf's more of a Rival but if you want to argue that go right the [tornado fang] ahead.
Yes, his relevance only ranges from fundamentally altering the main protagonist's entire life up prior to any game, up until the most widely acclaimed 2D entry in the series (and the only two chronologically later games, both of which he still appears in, are not well received). That's not compelling at all.
Wolf is...not worth it. I will say, though, an "antagonist" can take many forms outside of the traditional villain, and Smash has more than a few other antagonists (Wario, Dedede, Meta Knight, Mewtwo).
I'll also say this: Ganondorf is thematically the "most" overarching villain in the Zelda series, but even he has sat out a story arc or two. As for Bowser, there IS no overarching story to the Mario games. Bowser is "merely" recurring, what justifies him is that by the nature of his series, that's as significant as he needs to be. And he is not above stepping outside of the traditional villain roles if a threat outside of himself should rear its head.
Consider then, that the Metroid series, while certainly darker and more serious, isn't really much better than Mario at telling a story. And when it does try to, Ridley is near always part of it. He is the reason Samus was raised by the Chozo, which in turn made her what she is (super-athlete, Galactic Savior, etc.). More importantly, he is also the mainstay of the Space Pirate forces, who pretty much ARE the main antagonists of the series in the sense that basically everything that happened outside of Fusion either involves or was set in motion by them.