Crono is sort of like Banjo in that they have a legacy of affinity and are well-regarded, well-liked characters people would be happy to see, and wouldn't strongly protest the presence of. But they're unalike in that Crono isn't extremely popular in the way Banjo was, which is within the fanbase. Things are going to have to shift drastically in his favour to end up in the position Banjo was in. Otherwise he's just going to remain a darling within certain circles but a character not really at the forefront of anything anymore.
And to be fair, Banjo would've been included a long time ago had Rare and Nintendo not parted ways. What really drove Banjo's popularity is the history he had with Nintendo, and as one of their characters. Crono has a history with Nintendo, but a much more standard one for a third-party.
To that end, I do question whether Nintendo history is really a pertinent factor. Think about it. Nintendo history can inform demand, and demand affects inclusion. So it indirectly can matter. But look at the inclusions with the very strong Nintendo history. Mega Man, Simon, Banjo... these are the characters explicitly included due to the demand. I guess you could make an argument for Bayo, but until Nintendo adopts Crono, it's not really applicable.
And just having some key titles on a Nintendo system at some point is a pretty weak litmus test for history, considering most if not all of those examples, like FF, SF, DQ, etc. can also apply to Sony.