The monsters are the same throughout. However, there are, of course, dungeon specific enemies. Also, I didn't think the puzzles were overly the same.
I have to wonder about what John says about the instant kills getting boring because they are the same for that same type of enemy. God of War did the same thing and I don't hear anybody complaining about that. But anyway, I found this game to be pretty fun, if it does have some similarities to Zelda, but what game doesn't? LoZ practically invented most RPG elements still in use today.