At the same time, they can also be interesting in their own right, especially if you want to see how different things might merge and interact with each other.
Would Captain Kirk be very confused by Doctor Who, or Optimus Prime showing up on his ship, yes. Would it be interesting, but also cause the writers no end of headaches? Also yes.
I think Reason 2 might actually be a fairly good story in and of itself. You have someone who was an extraordinary being in their originating universe, suddenly finding out that they're just another superhuman in another. That would be an excellent point of character development, and a way for them to be suddenly placed into a completely new perspective.