Look at the first three rows, before the proto-echoes, third-parties, and DLC. The characters are broken up into two categories: series with multiple characters, and series with a single character (all of Mario seems to be treated as one unit). Now, Sakurai, being Sakurai, ordered these two categories by the debut of the series. Mario -> (DK maybe) -> Zelda -> Metroid, etc. for the series with multiple characters. The last one is Pokemon, the most recent with multiple characters. FE and KI precede it, even though they were added later to Smash.
The other category, the series with sole reps, is ordered the same. G&W -> Little Mac -> Duck Hunt -> ROB -> etc. all the way to Shulk, who is last. If Sakurai believed Shulk stemmed from the greater "Xeno" series (which isn't a thing), he'd have put him before Villager. Even if he started with Xenosaga, he would've put him before WFT.
"Xeno" is not a thing, at least for all intents and purposes in the Smash sphere.