I'd say the universe portrayed in the PT is visibly larger in scale than the one in the OT (more "exotic" planets and wacky aliens, that galactic senate mushroom, the overall scenery etc.), it's the STORY with its CONTRIVANCES that comes off as EXTREMELY UNBELIEVABLE.

Maybe it's just me, but when I see Kirk hit on College-Uhura in a bar, I don't think "wow, this universe is really SMALL", that's rather what I think when characters zip around from star system to star system without FTL - I just think, "wow, now that's convenient".