In defense of the Paper Mario 2 end boss finale.
While I feel it wasn't set up as well as Paper Mario 64 the turnabout after the feeling of helplessness in first part of final battle, but the lore kinda implies the Shadow Queen was playing with power she did not understand when she crafted the crystal stars to "to hold the essence of the heavens" ... I wonder if they might be less refined take on the principles of the Star Rod. It seems almost weird to think of it being made instead of always existing but you must remember the Star Spirits have a whole little society. And Kammy Koopa herself understood the principles enough to combine magic and technology to make a countermeasure, showing the principles can be learned.
So the Crystal Stars (or Star Stones in Japanese) are a more erratic and volatile primitive take on the star rod, created by one person unlike the presumed group effort of the Star Rod.
To break the fourth wall like the games: If the crystal stars react to praise like how Star Power is charged, I thin ihe reason the stars turned on the Shadow Queen is this time she didn't have an army of sycophantic monsters cheering her on like in the legends, while Mario had the audience.