And for that, I'll give Shadow Queen some credit. She manages to instill fear AND retain it. She is actually tough to fight, and she can very easily screw you over. She is one of the best boss fights in the series I've seen, and she is pretty fun to fight.
You can use Mega Rushes to win really easily and consistently tho
Again story =/= gameplay and I usually wouldn't give a character extra credit because of how the battle system works. The battle system can be good, entertaining, fun, and challenging, and that's one thing, and the bosses can be cool, evil, and intimidating, and that's another thing. I've posted my VG char fav list several times on this site, and for that list I didn't take anything to do with gameplay - how the character controls, how useful they are for platforming or combat, how hard a boss fight is - how regularly they are playable, into account, just their personality, emotions, design, dialogue, and role in the plot. Music probably doesn't count either tbh.
Grodus isn't my favourite villain by any stretch, but I still appreciate his existence.
And the X-Nauts at least are from the moon, and are a strange species unlike anything in the Mushroom Kingdom, so the Shroobs could come to the moon or the X-Nauts could go deeper into space and team up and that could work somehow. I haven't played PIT myself but I know that the Shroobs were an evil alien society so that would be cool imo