Well, knowing the writers of the mainstream Mario games, we're probably right.
Not having to split the spotlight among sidekicks is always cleaner than splitting it among seven. Again take a look at NSMB. Theoretically, the Koopalings could operate identically as minibosses in the towers (and you know they would). But there are more than seven towers. I think there are more like nine or ten. And the pre-final battle sequence would be a nightmare with seven Koopalings all gathered to throw Bowser's bones in that cauldron. And don't forget, Bowser Jr. fights in that last battle as well. You'd never beat it if all seven were all over you.
And in Galaxy, there was a huge number of original bosses, and Bowser Jr. only appeared about three times.
Just the facts. Seven villainous sidekicks just can't get appropriate screentime.
As a character, Bowser Jr. doesn't have too much going for him, at least not yet. But c'mon. In Sunshine, EVERY speaking character was annoying. In most games, his recycled voice clips aren't too good. But he got better ones in Galaxy, and I hope they go with stuff more like that for future games. He's not as good a sidekick for Bowser as Kammy Koopa, but I can't picture her in a game that's not Paper Mario. And I have faith she will return--she was probably excluded from Super Paper Mario just because of how unnecessary she was and how very little screen time she'd've gotten. Toad gets his "omg Mario help" role back probably for nostalgic values and because starting it off with Parakarry delivering a letter wouldn't have worked.