Completely different enemies doesn't guarantee that they will function differently than the bokoblins. I have a feeling that they COULDN'T come up with different enemies therefore they simply gave us bokoblins that function slightly different, honestly I find that cool.
I doubt that. Twilight Princess saw over 70 different types of enemies, if I'm not mistaken, so it's not like Nintendo is incompetent with monster design. However, the reason it had so many was because they focused on enemy variety. In Skyward Sword, they focused more on enemy depth. If you're not sure what I mean by that, I'll explain.
Prior to Skyward Sword, Nintendo always focused on having a relatively large amount of different enemy types that generally required one or two specific methods to be defeated. Enemies were pretty one-dimensional, but that was made up for in the sheer amount of different types. However,
in SS, they focused on fleshing out each enemy type's mechanics and abilities so that encounters with them were more dynamic, as well as increasing the ways they could be approached.
It's not that they couldn't come up with anything else, it's that they didn't WANT to. They wanted to make sure the more dynamic swordplay wasn't wasted, so they went with a smaller amount of enemy types than usual, but in turn, made them more advanced than usual. So even though there were less enemies than in past games, with the exception of The Wind Waker -- which I find weird, since that game didn't focus on enemy depth... although I guess it doesn't matter regarding this topic, either -- the game made up for it in the amount of choice that was made available in the combat. In other words, the polar opposite of what Twilight Princess (and most other Zelda games) did.
...All of which basically means Nintendo didn't run out of ideas.