There were quite a few enemies that I didn't like in Skyward Sword.
First of all, the Beamos; it was not that it was difficult per se, but that I could never get the stabbing motion to work in Skyward Sword, and of course, you had to stab the Beamos to finish it off; also, its laser beams were quite irksome, especially after a failed attempt at a stab.
Next in line was the Sentrobe. It bothered me because it was impossible to kill (correct me if I'm wrong on that, but I tried many different methods and none worked) and basically all it did was get in the way. This was especially an annoyance in the Lanayru Mining Facility when you had to do certain things with items and whatnot and the Sentrobe would attack you and you could not attack it back; you could defend yourself, but not kill it.
Furthermore, going with the electric theme (the electric enemies really are annoying), the Technoblin was also an enemy I disliked. Every time you messed up a swing with your sword and missed its weak point you were electrified, which both dealt damage and caused a pause to occur in an already tame battle of waiting for the Technoblin to move its sword so you can attack it.
Additionally, the Skulltulas were incredibly annoying in Skyward Sword. Getting them to flip over was a pain. One profound instance of this was in the Skyview Temple when you had to kill the Skulltulas that hung from the ceiling; you had to essentially slash at them and hope they'd go back to starting position turned around so you could deal them damage, but all the while you were hoping that they didn't swing back and hit you, knocking you off the narrow walkway you stood on. I was stuck in that room for quite a while and it bothered me a lot.
Also, the Quadro Baba was pretty annoying. The Deku Babas already had the right amount of difficult in my opinion, and adding more was just a little too much. Take into account that, as I mentioned before, I thought the sword motions were a bit glitchy at times, so enemies such as the Quadro Baba were a real pain. It's not that they were hard to defeat, but rather that they took too long; there was too much wasted time in the wrong motion causing you to wait for it to open up again, and the fact that it had the pattern of opening either vertically or horizontally at will added to that.
Finally, the Sacred Realm Guardians were irksome to me, as well. I thought they were much more difficult to avoid in contrast to the Phantoms of Phantom Hourglass and Spirit Tracks; not that difficulty is a bad thing, but it felt to me that if you weren't under the protection subsequent to obtaining a Tear, it was practically a sure thing that you would be killed by one of the numerous Guardians. I appreciate the difficulty, but just a touch less in that regard would've been nice.
As you can see, I disliked a lot of the enemies in Skyward Sword. There were plenty I liked, but there were probably just as many I didn't. Though despite annoying me every time I ran into them, these annoying enemies didn't take away from the game as a whole too much for me.