I know Samus didn't speak in the Metroid Prime games, but she totally narrated Super Metroid, Metroid Fusion, and Metroid Zero Mission, and the first two were at a time when almost no characters in those kinds of games spoke (Mario, Zelda, etc.) just because it was hard to do. She even had several heated arguments with the computer in Fusion!
 
She ain't a silent protagonist. That's a fallacy that keeps being perpetuated. She's also not a snotty brat like Other M. She's confident, powerful, and deadly. And she freaking talks in all the games that matter. I give Metroid Prime 1 and 2 a pass since there was technically nobody to talk to, but I was mad about MP3 not having her speak.

She said not a word in Metroid one. That makes her silent. Then, she talked in sequels. Thus, she does belong.

Debatable.  I'm curious as to why "The Boss", of Saints Row, is not considered to fall into this category.  Technically he does speak on four occasions in the game, but all of his lines are just witty, humorous statements with no bearing on character development or the plot.  They're little more than rewards for the player completing a portion of the campaign.  In the second game, he won't shut the hell up, and this deviation outlines that the previous game featured a silent protagonist.  I think the discussion is always going to have some inconsistency over things like Samus' status, and the one I outlined.

I don't know if everybody on the NES were silent. Like dude from Power Blade says "Let's torch this place and get out" at the end of every level. I think there were a lot of dudes that talked in intros or cut scenes if the game had them. I get that you don't want for people to think of her as the character from other M but I don't think that many people actually played the game for that to be so. Don't worry.

This category as a whole seems kind of convoluted to be honest. Not talking is largely a limitation of tech, or it was for about 20 years. Its only been an artistic choice for about 10 years. Its like going "3d games that used to be 2d". That would be any old game that got a newer version later.

I agree, I don't think she belongs, because the wording of the concept makes it sound like it's for characters who originally didn't talk, and then did in later games. It's not "Characters Who Talk In Some Games But Are Silent Protagonists In Others." 
 
EDIT: Did not know that she was apparently entirely silent (no narration) in the original Metroid, in which, I guess she does fit.

Samus didn't have any dialogue in Metroid or Metroid II, thus she was a silent protagonist.  She didn't have any lines until Super Metroid.

Brings up an interesting question. A lot of characters from older games weren't voiced simply because of technical limitations, not design choices like Jak from Jak & Daxter or Isaac from Dead Space.

Cus I mean, Link grunts and such. And Mario uses words but in the same kind of context, never actual speech bubbles. Where is the line, you know? Seems to interpretative imo.