If Elibe was going to get representation I don't think that Lyn would have been an AT. Honestly, I think Fire Emblem will only have two reps again, and it will be Ike and Marth; old and new basically, which was the same as Melee had, regardless of advertisement.
Roy was fresh meat of the FE series, and he was put in Brawl for that reason. Ike is now the fresh meat and has taken that place. Marth is the classic, loved lord of the series and he will be back for that reason, as well as the fact he has starred in more games than any of the other characters.
Now, if by some miracle the series did get a [well deserved] third rep, the biggest issue is not that one of the continents from the series should be represented, but do they want to put emphesis on the classic Fire Emblem (FE5 and older, you could probably count 6, but I am not because the story tied in with 7), or the newer, and more current Fire Emblem, which would be FE 6 and later.
Classic Fire Emblem is generally considered "better" but at the same time, they may want to push recent characters to show what the series has now. It's a very debatable subject.
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Since this topic is about Roy though, I will focus this on him. FE6 did have sales, but beyond sales the game was not as well received as others, including the more recent games like FE9 and 10. A vast majority of Roy's popularity came from Smash Brothers, and not his own FE game. This is his first real problem.
The character is meant to represent the series they are from, and not the character itself. Don't take this wrong, the characters are meant to portray themselves from their games, but they also want proper representation of the series. Without his Melee fanbase, Roy would just be another no name FE lord that would not even be considered.
Also, as I mentioned above, he WAS the "new" of the series. That is why he was added. Roy is no longer new at all, so the whole reason he was put into Melee is a null point that cannot be used for him this time.
Basically, I think Roy is out. But if they do add a third playable rep, it's up in the air whether they would take FE history, or FE of today. That is the biggest question.