I hate to be the one to say this, I love metroid and much prefer the giant buff samus depiction you linked to ZSS; but imo the games that really brought on the 'waifuization' of samus are echoes and zero mission, and they came out in 2004. That's 20 years ago, they're closer to NES Metroid (1986) than now.
Doesn't matter that they are closer to the original games than now. Canon dictated from the beginning, and with only a few anomalies of games contradicting this, that Samus was not quite "Amazonian" in stature. She's a 6 foot 3 inch/ 192 cm tall blond haired bombshell, that also weighs enough to go toe to toe with the absolute worst threats that the galaxy has to offer.
Admittedly as a 6'3" tall guy, I do wonder about her only being about 200 lbs, since I am about 30 pounds heavier at the same weight, but I suppose I was lighter when I was in university and the USN.
Trying to make Samus into a pixie waifu character would be like trying to make Tinkerbell into a punk pirate that followed Captain Hook, or trying to turn Harley Quinn into a perfect conservative housewife. The ideas are literally antithetical to the original character.
How in the world is a 192 cm tall, and 90 kg woman small?
Hell, I'm 192 cm tall, and 115 kg, and most people tell me that I'm tall and "athletic" despite me having a "dad bod," with an IMO considerable gut. Admittedly I do miss the 8 pack I had when I was 14-24 years old, but I was painfully skinny and swimming my ass off literally to achieve that.