For the season finale, the opening credits were changed so that they would reflect life in the alternate universe - throughout the episode there was a "red" motif, to the point where one might have thought it was the world of 'The Mentalist'. (For instance: there were comic books about the super-heroes Red Arrow and Red Lantern.)
As such, the opening credits were tinted red instead of the usual green with blue highlights.
But there was one other change in those credits:
"First People" - I think we have a clue to one of the plot-lines for next season. Could it be that in the alternate universe they have definite proof of alien visitation to their world? Or maybe it's a reference to the main Toobworld being the original dimension? Or was there a separate line of evolution that didn't die out and developed alongside homo sapien?