You're thinking more along fanbase and less along ACTUAL sales. Square-Enix is a business foremost and always.
Now, if a 9 year old just unlocked Geno, would he say either "Oh wow, it's Geno from Square-Enix!" or "Hey, this doll dude looks cool!". Geno is mostly a cult favorite, and yes, the polls do show he's a popular character. Hell, if I was able to vote, he'd be my first choice for a third party, considering I don't really like Sonic, and I just plain hate Megaman.
Squenix wouldn't get represented by a character that hasn't been used in a long time, and UNLESS Nintendo bought the rights to Geno, Sakurai going to them with a check in his hand wouldn't cut it. See where i'm going with this?
Also, what are the chances of Squenix even getting involved with Brawl? Third parties are iffy, the only reason Snake is in is because he was an easy add-in, and it cost Nintendo absolutely nothing.