The difference between Samus and Link is simple: Samus is a single, defined character. Link is not.

Who Link is changes with virtually every game. Almost every game features a unique Link from a new reincarnation cycle, sometimes even in a completely different time line, who is never given any characterization beyond being the "hero". Even in his newest games, I've been free to give Link any kind of internal voice that I please. Maybe he's a genuinely nice guy, maybe he's a dick who likes breaking people's pots. Who knows? The beauty of a silent protagonist who isn't given much characterization is that the player is pretty much free to make him or her whoever the player wants, even in games that strictly limit what you can actually do.

Samus was in the same boat until Metroid Fusion and Other-M where she was, for better or for worse, given a voice and a character. We now have a pretty good idea of who Samus is, and she is now not so much an empty vessel as she is someone who just often doesn't have anyone to talk to. Indeed, one of the primary reasons why so many people found Other-M so alienating was because the character in the game was not the character many players had imagined for the last 20 years. Many players had their own idea for Samus, despite the fact that she didn't really HAVE any character before, outside of Fusion.

So, I'd disagree with the notion that Samus is more of an "avatar" then Link. Besides being the same person in every game, Samus is a defined character.

Now, if Fusion and Other-M did not exist, there could be a stronger argument for giving players the ability to customize Samus's sex. But there are still two issues here:

1. As you said, we don't really see much of Samus outside of the suit (aside from Zero Mission and unlockable sprites after beating the games), but the suit is pretty gender-neutral, so what would be the point? The gender of Samus isn't even revealed until the end of the first game, at 100% completion. And speaking of which...

2. Unlike Zelda, Metroid does something few other 8-bit games did: it flaunted the gender of its character. For many NES players, finding out Samus wasn't a man WAS one of the game's memorable moments. I've seen it mentioned enough times by nostalgic NES gamers to know that. For better or for worse, the gender of the character became a part of the identity of the Metroid franchise. Link, on the other hand....has always just kind of been a guy.

These reasons are more superficial, yes. I would have FAR LESS of an issue with a male Samus under these conditions, but its still not the same situation as Zelda.

Part of what makes "female Link" work for me is simply because the game has a variety of unique factors come together: Link is a gender neutral silent protagonist with only the vaugest of characterization, who isn't even the same person from game to game. The Link in the next game will quite literally be a brand new, different person with none of the past Link's experiences. He's going to be kept silent so that players can fill his vessel however they please. So why not allow players to customize that vessel? Why make him consistent with every other Link? ]

Mario doesn't really have much characterization either, but I'm not advocating we give players the option to give Mario boobs because, alternate dimension versions aside, there is only ONE Mario.

Any other game that does what Zelda does gives players the ability to at least select gender and skin color these days. So why not Zelda?

One great thing about allowing for customization of Link is that they could TOTALLY let you slap a bad-ass beard on him.