Pardon if this question is vague or misguided, I'm a CS person who only dabbles in math.
In a groupoid all morphisms are isomorphisms. So then, any two objects with a morphism between them must be isomorphic.
So then isn't the only question that matters in a groupoid the question of whether two objects are connected at all? If they are connected they're isomorphic and in the same equivalence class, and if they're not then they're in different equivalence classes.
If you skeletalize a groupoid, it seems to me that you'd just get a bunch of groups sitting next to each other, not talking. I'm wondering -- is this correct, or is there a subtlety I'm missing? And if I am correct -- what's the practical benefit of talking about a groupoid, as opposed to just talking about a collection of groups?