There are multiple reasons.
Defensively, Grass/Dragon isn't a great typing, though it's supposed to be a tank. Even with Thick Fat, it's best defensive ability, it still has 6 common weaknesses. (Ice, Poison, Fairy, Flying, Dragon, Bug.)
Appletun is extremely slow, at base 30 speed. While it does have a high HP and SpA stat, it's SpD and Def are mediocre at best.
Appletun has an okay movepool. Most of the moves it learns are Grass, Dragon, or Normal. (Go look at it's level up moveset, it has absolutely no coverage. The only moves it learns that aren't Normal, Grass, or Dragon are Withdraw, Iron Defense, and Curse, which are all status.) It can learn some decent moves from TM/TR, like Gyro Ball (Good with it's bad speed), Giga Drain, and High Horsepower. But that's pretty much it.
Even it's signature move, Apple Acid, can't save it. It's almost always better to raise your own stats than lower the opponent's. With the 100% chance to lower SpD, Defiant or Competitive users could switch in and reap the benefits, especially if Apple Acid is it's only attacking move.