Is hyperbeam Mewtwo that bad?

Yes. Go for Focus Blast which is SE against the best defenders

Hyper Beam isn't a bad move for Mewtwo because of its stats, it's because of its typing. Normal type isn't SE against anything.

From a neutral standpoint it is not a bad move at all, even coming in second as you mentioned. However you are giving up potential super effective damage which will then make HB look worse.

Unless you find yourself wanting to use Mewtwo to tackle both Normal types (shadow ball fails) and flying types (focus blast fails), then you'd be best to choose one of those two. Even if you choose HB, you'll get walled by Rhydon and Ttar- two reasonably common gym defenders.