Yes, it's subjective, but there is one individual in particular you need to worry about that subjectivity with: Sakurai. His definition of fun decides the fate of every character on the roster, and we've seen it swing against something as big as Resident Evil and yet in favor of Joker. Obviously, you can pick apart all the individual differences of that situation til you're blue in the face, but it proves that such things are possible and Sakurai's definition of fun doesn't always manage everyone else's. I thought a Resident Evil character would be a blast, but Sakurai clearly didn't see the same conclusion. And there is also the issue that, KOS-MOS is arguably filling an extremely different niche from most Bandai-Namco picks. She's part of the greater Xeno universe that Monolith Soft has worked on and nurtured for ages now. It's extremely unlikely that she "gets chosen as a Bandai Namco character" as that's not why people are interested in her. She fills a different niche than many options, and there is undeniably a demand for more love given to the Xeno series in Smash. We've seen the love and support for Rex/Pyra/Mythra and Elma, and many of those same fans are here championing KOS-MOS as well.
Xenosaga's profitability can be different from KOS-MOS in Smash. Lucas was deemed important enough to be DLC in Smash 4 and Nintendo couldn't even be bothered to localize Mother 3 anywhere. Robin was still chosen as an additional fighter in Smash 4's design document despite the fact that the series was literally hanging in the balance profitability wise (in 2012, Awakening was the make or break moment for Fire Emblem since it was looking bad for the series, which was also when the project plan for 4 was developed and Sakurai had no way of knowing Awakening would be that kind of a success). There's precedent here that characters in Smash are not necessarily bound by the profitability of their parent franchise. Hell, Banjo & Kazooie got in despite the fact that Microsoft is perfectly fine with the series staying dead and investing exactly nothing into it.