One thing that annoys me is how such a large percentage of legendaries are Psychic type. I don't know much about the D/P legendaries, but there are certainly enough Psychic-type legendaries in the first three generations. Are they implying that this type is "superior" to other types?
Another thing that annoys me is how Charmander and Cyndaquil (and their evolved forms) have the same base stats. The only major differences I see are their first evolution levels (16/14) and their slightly different movesets. It's bad enough that they're the same type (Charizard excluded, since it has a Flying element), but do they have to have the same base stats and practically the same movesets as well?
I guess the fact that they're in different breeding groups adds a bit of variety, but still, two Fire-type starters with identical base stats is a bit much.