I remember liking its story a lot back when it released, the ending gives a twist to us who have played all the previous PMD games. The nods to older characters in the link/friendship system were nice as well.
What I disliked was the level scaling. Why do battles give you so little EXP? It's almost imposible to level up, you're basically forced to use the higher-level recruited Pokemon instead of training your current ones (including the MC and its partner) for the post-game missions and dungeons. The fun of PMD is to play as any Pokemon you want, but Super made it imposible...