It's really not unfair, you just have to be a little more strategic. You'll have to more or less 'expect' Shedinja to show up in either the Bug-, or Ghost-type rankings, why not change one of your moves for both of those sets of 10? It won't effect your streak and you could say, add a Fire-type move to better combat the Bug-type section.
I did something similar in my 182 run with Garchomp. There is an Infernape in the Fire-, and Fighting-type challenges, it has Fake Out. I was using a Focus Sash Garchomp, but during the Fire-, and Fighting-type challenges, Fire Fang would be useless and Infernape can just break my Focus Sash then possibly OHKO me with Close Combat. So I simply switched the useless Fire Fang for Protect so I could Protect first to prevent Fake Out, then safely KO Infernape with Earthquake with no fear of being OHKOed in return. Low and behold, Infernape was the Rank 10 on both Fire, and Fighting, so it was a great decision to edit my moves.
Use this to your advantage.