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A main problem is the moves themselves. Ice Beam, Surf, Flamethrower, Psychic and Shadow Ball are some special base 90 moves, but although lots of types get a variation of it the other types don't get any at all like Dark and Ghost and have stuff like Shadow Ball for their best STAB. Of course, this is merely a case of the move not existing yet, so there's a chance it could be introduced later.
Then you have stuff like Power Gem, which are a variation of the standard 80-90 base power move, but due to what the attack involves (gems in this case) Pokemon like Magcargo and Omastar miss out on a valuable STAB. Poor physical Electrics have to deal with Wild Charge because Pikawhore took their Flare Blitz variation with Volt Tackle. This problem is worse than the first since you probably won't get another move like that, though if lucky there might be a new move that's almost as good (Sludge Bomb and Sludge Wave, Flamethrower and Heat Wave).
