Every time I raise the issue of Samus' sexualization, I'm reminded of how it's been a part of the series from the first title, with her bikini reveals at the game's end. That may be true (though I'd argue that with the NES's limitations, that was the most effective way to communicate that Samus is a woman at the time), but I don't think that's what got most people into Metroid games, or even vested in her character (beyond initial titillation, something I imagine is pretty much nonexistent for players who learn it for the first time nowadays). At the very least, Metroid, Return of Samus, Super Metroid, Fusion, and Samus herself weren't sold to me on the promise that there's a supermodel under the suit.
The debut of the Zero Suit kind of bothered me, for although it is indeed a practical garment to wear when within mechanical armor, I got the distinct impression that that wasn't why it was designed. It felt like a cheap way to generate interest in the franchise, and it bothered me that Metroid had to resort to that. It also felt like an indignity toward Samus herself--that they decided they couldn't sell the character on her bravery and prowess anymore. I also felt like it took away some of the mystique surrounding Samus, like any other costumed superhero. I did like the "her entire arsenal's been taken away from her, but she can still hold her own" scenario, though, even if did seem to merely be riffing off the stealth game craze of the time.
Today, I'm over the Zero Suit itself, but take issue with Samus's physical portrayal. It seems like with each new iteration, she gets younger and younger, and looks more and more like a swimsuit model. I have nothing against swimsuit models, nor am I saying that swimsuit models can't also be physically capable--but we're talking about a galactic bounty hunter here, who earns her keep strong-arming her way through labyrinthine hostile environments and going toe-to-toe with deadly beasts. I'd expect to see a little more muscle on her. "Because Chozo blood" doesn't cut it.