IN most basic terms, the differences are the size and shape of the gearbox. To accomodate different body styles, different mechboxes are required. And of course, different sizes and shapes require different internals to match, but basically, all main internal part are identical and perform the same function.
Some mechbox designs are structurally stronger than others. A V3 mechbox shell tends to be more durable because of its shape (more solid metal at the tip that takes all the impact). It has more metal holding the cylinder head in place. A V2 has less metal holding on the cylinder head, and has tendency to crack after prolonged use because of that.