While there are different routes, they all start in the same place and they all end in the same place. The differences in difficulty comes not only from the number of stages, but the difficulty of the individual stages and what characters you can meet. Regardless of which path you take, you will have to go through stages 1, 8, 9, A, and at least part of 3. Stage 2 is optional and accessible on all routes.

Once you defeat Dracula, you will restart the game.
While it may seem like exactly the same thing at first, it is significantly more difficult, due to having additional enemies. Other than Japanese version, there will also be new enemies which act differently.
You begin the game with the same helper that you finished the first quest with, allowing you to get through the early stages in different ways and reach a few new items. Notice that you will not encounter any new helper in this mode. If you manage to beat the previous game with Trevor alone, you will not have a helper for the entire second play through. Good Luck!