Right, before I go to bed, I'll leave this here. This happened while searching for game logos:
My favorite FF characters: Boss and Shadow.
For real now, time for me to go.
Ivysaur also doesn't have arms, yet it's in Smash. Suicune doesn't have arms, yet it's in Pokken. Pikachu barely has arms and attacks mostly with its body in both, Smash and Pokken. Not sure how Exeggcutor is being a problem. If anything, a Pokemon fighting game should be varied, playing to the strenghts and abilities of the various fighters. If all had the same body shape, might as well just play another generic fighting game instead.
Seriously, Exeggcutor has enough to pull from, even without hands: Hypnosis, Barrage, Egg Bomb, Stomp, Headbutt, Wood Hammer, Bullet Seed, Giga Drain, Psyshock, as well as generic body blows and kicks.
Pokemon are magical creatures which can shoot beams of energy and change the weather at will. A lack of feet or hands is not an issue at all.