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What I missed about X was the trainer customization. Serena had a ton of choices available to her compared to Chicken, and I missed the hoodie and baseball cap options Calem had. Dying clothes is nice and all, but the clothes themselves don't feel as unique as they did before.
Festival Plaza also feels terrible compared to the PSS. What I liked about the PSS was that you could continue to play the game normally while still getting trade requests while you play, or quickly access it to get to the GTS or battle a friend, and you could set your own messages rather than being forced to use presets like "I'll get a shiny!" which doesn't help when you're asking for specific Pokemon. I'd rather have the Festival Plaza be something separate instead of trying to integrate both the PSS and the Join Avenue at the same time.
I still enjoyed Moon a lot and thought it was a good game, but these two things were what bugged me a lot.