I think the thing with Bowser feeling sidelined by a new villain is more related to how business as usual is interrupted whenever a new villain comes in, as the new villain has their own agenda unrelated to the usual conflicts between Mario and Bowser. Bowser is probably used to Mario (and Luigi) being his only adversary too, so a new face in the mix throws the usual routines off for everyone. Bowser is an important part of the main cast, which is why it's hard to just inexplicably have him absent for the sake of the plot.
I'm actually still slightly worried about the M&L series post-remakes.