There's a lot that falls apart with this response when you look at it.
Yes, KOS-MOS may no longer be owned by Monolith Soft but she is still considered a Monolith Soft character as depicted by this corporate anniversary artwork. Despite the copyright ownership of KOS-MOS and Rex being owned by Bandai Namco and Nintendo respectively, they're both Monolith Soft characters.
Then we get to your argument about DLC characters from pre-existing series or characters from similar enough series with Roy and Byleth. What you've just done is compare the DLC roster of Smash Bros Wii U/3DS to the DLC roster of Smash Bros Ultimate, two different games. That's not a logical comparison. And yes, whilst Banjo Kazooie's inclusion doesn't prevent Yooka Laylee, let's be honest here, why would Nintendo have Yooka Laylee as a DLC fighter?