If you are going to use the "she isn't the most important" line against Sami, you might as well also use it against Lyn, and unlike Lyn, Sami does have equal or greater importance in later Advance Wars storylines.
Also, as others have previously mentioned, Sami's connection with infantry and her canonical depiction of:
1. Being a member of Orange Star's specical forces.
2. Being depicted with realistic weapons.
Makes her plausible to have a derivative of Snake's moveset, and considering how the Project M team is pressed for time and staff, this makes her particularly atttractive, especially in comparison to other potential new series newcomers.
I'm not using it as a point against Sami, but rather, a point for Andy. Let me try to explain my perspective a bit better.
You're saying it's Sami's moveset potential as a Snake clone that makes her the better choice, and that makes sense. Andy, I've heard, is more of a support character and doesn't canonically use the kinds of weapons he would gain from Snake.
However, this is why the Earthbound analogy is a good one. Like Ness, Andy specializes in support and healing. Like Ness, Andy could borrow from his comrades. Smash has never cared about canonical abilities, as many characters can attest to. Is there anything Sami can do that Andy is just physically incapable of borrowing from her? Unless I'm greatly mistaken, there isn't.
Looked at from this perspective, Andy and Sami could have equal moveset potential. Their status as a main or support character isn't a point against Sami, it's a boost for Andy. Sami gets a pretty big boost of importance for her popularity and for being a major characters, but historically, the face of the series wins against more popular characters. (Marth and Ike, both main Fire Emblem characters were chosen over Lyn, for instance. It's not that there was anything wrong with Lyn, she just wasn't chosen because there were characters with more importance.)
If one of them is chosen, it will probably be Sami because I'm sure PMBR will want to appeal to the fans and she's more popular. I'm just saying that historically, this is the way past Smash characters seem to have been chosen.
I understand your position, and I hope I've explained mine well, but I don't really see any point in arguing further since we both seem set on our preferred characters. I'd like to just agree to disagree.