Additionally, that's an excellent list of characters and would LOVE for Klonoa to be added (totally forgot about him and I feel ashamed as a result). For some reason I would think KOS-MOS being added would cause friction with Squeenix and the rest of the those mentioned probably wouldn't get past Nintendo because $$$. It ought not be that way but it probably is why characters like Shantae and Shovel Knight aren't already in (the latter having significant amiibo support already).
IF there was any additional Namco love to be had...Klonoa would be my pick but I wouldn't be upset with Dig Dug's inclusion. I figure Stahn Aileron from Tales of Destiny or the protagonist from Symphonia could be considered. I tried to think up someone from SoulCalibur or Tekken, preferably female, but outside of Mitsurugi and Kazuya, no one really stood out. Since people are all about Sephiroth being in and there being a need for villains, Kazuya would probably fit that bill perfectly.
Lastly, just saw that a Ghosts 'n Goblins remaster is coming next year and I think Arthur would be a great addition to the game.
If ownership is what you're inferring, Square-Enix has no control over KOS-MOS given the character is entirely a Namco IP—Xenogears and Xenosaga are unrelated, other than sharing "xeno" in their name. Monolith was originally created with the intention to expand on Xenogears, but as we all know that never came to be and Xenosaga ended up materializing, with Xenoblade taking over the reins after the latter's third episode. They're still both considered spiritual successors to Xenogears, Xenoblade more so in more ways than one.
As far as characters go, I think Dig Dug, Klonoa, or Valkyrie would fit the roster rather well, so I'd be happy with the inclusion of either of the three. Regarding Soulcalibur and Tekken, Yoshimitsu could represent both series and actually seems like he'd fit rather nicely, too; but if you'd rather have a quirky character, then Mokujin from Tekken seems about right.
Villain-wise, Sigma has always been my choice, but admittedly is a very biased one. I think Dr. Wily and Dr. Eggman would make a nice addition, but probably just one or the other seeing as they might end up using some type of machinery to battle, although the game already has characters that play similarly, so that might not matter at all. Lastly, a bad guy from Street Fighter wouldn't hurt, which most probably would end up being M. Bison/Vega. And also, Waluigi.
And yes, Arthur would be a nice addition to the roster; he's as classic a character as any.