Agreed. I always found it a bit odd and disappointing that the Fairy Godmother wasn't that involved in the series after KH1. She was part of the people helping Sora too, maybe not so much as the others but still. I know she appeared in BBS but that was mainly for the movie plot. We didn't even get to see her and Cinderella reunite after Hollow Bastion.Also, it’s kinda poetic to have Riku meet the people Sora met and helped him a lot when he started his journey. The FF gang, then Merlin, then Fairy Godmother.
They would each have some sort of comforting or guiding words to set Riku on the right path.