Availability isn't that big of a deal in most circumstances. Special episodes places you in different areas of the region with different warlords and different Pokemon. You can easily get most Pokemon via warriors, linking or passwords. The exceptions to this are Swarm Pokemon and legendaries, which are based on luck and certain prerequisites, respectively. Not to mention Pokemon you recruit carry over and have their link reset. Availability should likely be ignored for simplicity's sake.
Another thing that is incredibly important to think about when ranking a Pokemon is what abilities it can get. Intimidate is amazing and getting it makes any Pokemon instantly better.
Also, for the sake of not becoming a mess, I think it would be best to avoid including warrior/warlord information when ranking Pokemon.