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Why is Lillie's Clefairy a problem, though? Lusamine raised Lillie - it is obvious her pokemon choices would reflect Lusamine's tastes unconsciously. Ribombee and Comfey also would have fit in well with Lusamine's team choice - being cute and beautiful. Lillie's pokemon doesn't seem too weird...
Introducing the Ultra Recon Squad and the Megalopolis, and then underusing them severely was a big waste of potential. I have a feeling that they could have taken out all the new characters and expand Colress's actions instead and the overall arc would have still worked somehow. Heck, it was...