I would guess that the ground weakness is a biggy as well. Lots of pokemon with access to strong ground moves like Earthquake.
Dark Pulse may be the best defensive move, but it doesn't seem like a great threat without STAB. Sure, it's super in to Psychic, but without STAB it's the same bonus as something that only had STAB. Plenty of Rhydon/Golem and various others (e.g. EQ Snorlax or Bulldoze Arcanine) that can presumably fight in to one with Dark Pulse quite easily.
Also the CP may be there, but the base stats may not. He may just not survive long enough to be a big threat. Maybe most Exeggutors can kill him before he casts his first Dark Pulse.
Disclosure: I've actually never fought against a Muk in a gym.
