No, rather than that, what I meant is: "You should design the natures around the waifumons", as weird as it may sound.
They're their own characters, and I personally would prioritize flavor/story over mechanical gameplay. So their natures should be who they are, even if it comes at the price of mismatching their combat viability. Still, that is my opinion.
However, have you considered that, as of now, this whole conundrum is not that much of a problem, since all the waifumons' personalities match their "meta" natures anyways?
Lonely suits Lopunny, Naive works well too. Maybe Adamant (the "best" one) is a bit of a stretch though.
Modest is perfect for Gardevoir (Quiet/Mild also work as second choices).
Bashful is perfect for Viruark, although it's a neutral nature, but all the Atk ones fit her just fine as well: Brave/Lonely/Naughty, and, of course, Adamant.