If you saved Luna from the Arceus cultist, being El, then the next place to go would be back to the Psychic Gym Leader's labyrinth outside his Gym and entering a tree, which would bring you to the next Gym.
I'd say Arceus, because there's very few strategies that can counter it, and you actually need to fight it and win (if you side with Radomus) unlike Garchomp.
Try using Growlithe with Flame Burst, which you can get from finding all 5 Police Officers. It can burn the field, changing it to something that won't be so beneficial to Shelly.
EDIT: Oh yeah, Fire Pledge does the same thing to the field.
http://www.pokemonreborn.com/forum/index.php?showtopic=18129 has all the wild Pokemon rates.
Answer: Yes, it was changed, since Bunnelby really is strong. 5% chance in both.
We actually can get Rock Tomb already, so cross your fingers for Rock Slide~ Anyway, yeah, that sounds about right. The end isn't too far; good TMs have to be given to us at some point soon.