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>Lack of player choice is definitely an issue.
>As well as the ignoring of the Pokemon themselves. The closest Gen 5 gets is with the Swords Trio where they choose the protagonist to wield them in battle.
>Pokemon are intelligent and basically sapient. That has been a constant throughout the franchise since shortly after Red and Green's release. The lack of interfacing with your own monsters directly in a story about, "is catching Pokemon good?", is a huge missed potential.
>Why not use the 'Dream World' mechanic to actually do something like talk to your Pokemon, with different results based on their happiness score?
