It's not really all that weird when you realize that those "protagonists of the first game in a series" are generally still part of said series down the line as protagonist or at least a major character (i.e.
being ironically in the "damsel in distress" role in the original DKC trilogy after the first title prior to the first Smash).
With series of rotating casts (which is pretty much the RPGs), it's more inconsistent as to who is picked first.
Marth is the protagonist of the first Fire Emblem (and third) and was picked. Now, he was the most requested one for Melee, but Sakurai was already considering him for the first Smash.
Ninten is the protagonist of the first Mother, but Ness got in instead, the latest of the two protagonists (and was planned to be replaced in Melee with the following protagonist, but we know how that went).
Cloud didn't come from the first Final Fantasy. He's just the most popular character in the entire franchise and was the most requested addition from it on the Ballot. And even then, other characters Sakurai mentioned from the franchise (Terra, Bartz, etc.) didn't come from the first game either.
Joker didn't come from the first Persona, he came from the latest. Hell, anything before Persona 3 isn't acknowledged, which is more notable than Smash strictly featuring Final Fantasy VII.
None of the playable Heroes come from the first Dragon Quest, with the default being from the latest one, and the earliest among the alts being from III.
Shulk does come from the first Xenoblade.....but at the time it was the ONLY Xenoblade so it's not like we could have had another protagonist over him instead. Can't really say one way or the other for sure if he'd have been picked first if for example, Rex and the Aegis were direct competition.
And even an example from a Mii Costume, Tales of Symphonia was neither the first nor latest in the Tales of franchise and yet Sakurai made it a point that Lloyd was a priority for the Mii Costume role out of all protagonists.