Some Pokedex entries are quite... questionable for me. Otherwise, I don't have many problems with anything else because:
- Pokemon are RPGs, of course they have RPG elements.
- Movesets and the likes are for game balance purposes.
- Some mistakes/oversights are too late to fix (like Mr. Mime), or maybe they don't want/too lazy to fix.
But ultimately, the fact is that:
Game logic ≠ real world logic