While physical attackers seem to always be disadvantaged, that is often not the case. Moves like Will-O-Wisp, King's Shield, and Spiky Shield and abilities such as Intimidate, Iron Barbs, or Gooey can often be easily predicted and easily countered by switching out or using the turn the opponent wastes on protecting to set up using Sword Dance or something similar.
Another point you made was that Cotton Guard seems to be detrimental to physical attackers. The same could be said regarding Amnesia or other moves that boost a user's special defense against special attacks.
While there are more physically defensive Pokémon, many of them function poorly. It's not about the quantity of the Pokémon that can perform any given duty, it's about how well they can do it. For example; Golem has a very high defense stat, but ultimately it's a Pokemon with no reliable forms of recovery and 4x weakness to common types. This makes it a relatively useless wall of any sort. The same can be said for most rock types.