I also see a weakness to (along with Arceus-Fighting and CM Arceus-Ground) Shaymin-S.
I guess you could try running Ho-oh over something; possibly Gliscor? It hurts you in the sense that you have nothing to beat RP Groudon besides Giratina, but Giratina is already a pretty good counter, and unless RP Groudon runs Fire Punch, Ferrothorn can check it in a pinch.
Furthermore, the Zekrom problem that will be opened up can easily be dealt with by your Excadrill; in a pinch, Ferrothorn checks it too, so it's not really a big problem.
Try running something like
Ho-oh @ Leftovers / Life Orb
252 HP / 252 Atk / 4 Spd (you can speed creep to beat Kyogre, etc)
By running Ho-oh, you can lure and weaken Giratina, Kyogre and Lugia; these Pokemon all stop a Excadrill sweep.