Some enemies in the game are quite annoying for me too, I'll go over them (since I'm playing the German version of the game, names might differ, I'm using names from previous Zelda games if possible):
Beamos: One of them at a time is OK, I have no big problems performing the special sword slashes (horizontal/horizontal/stab) but what I hate is when they gang up on you. There's one room towards the end of the sandship where there are three of them, I HATE that room! Normally when you have two of them you can at least make it so that one of them can't reach you (for example in the Pirates' Hideout where you can use the time ball so that only one of them is activated and then deal with the other one). But here, there's absolutely no blind spot! While dealing with Beamos A, it's almost guaranteed that Beamos B and/or C will shoot at you, and there's no way to avoid that, at least I haven't found the trick. And once you get shot from Beamos B/C, then Beamos A will use your knock-out time and shoot at you too, the only thing you can do then is to quickly leave and re-enter the room (while probably getting hit yet another time during the process). I finished the sandship in Hero Mode today, and I went into the room with full health (~13 hearts) and left it with ~3 hearts after using a full potion (had to use it when I was down to 1), so in total those annoying f's ripped me off around 22 hearts, that's ridiculous!
Electric Chu-Chus: There's just way too many of them, and when you split a big one into two and are not quick enough with the spin attack afterwards then they WILL electrocute you. Sure, you could wait for the electricity to go off but that takes to long, especially if it's a huge chu-chu that splits into 4 or 8.
Bokoblin Archers: This time around, they detect you from an extremely high distance and you have to look around to find them and shoot them with your own bow. You're likely to have been hit 2 times by them by the time you've located them. They're especially nasty when you don't have your own bow yet, for example in the Ancient Cistern there's a room where one of them is on a higher ledge. He can reach you but you can't reach him and you'll probably get hit when you're on the vines near him (before getting to him). And they are annoying in a certain escort mission too, there it's crucial to your success that you see them from miles away, so you have to stop and check your whole field of view thoroughly after every few steps.
Fat Spear Guys: (whatever their official name is, I'm referring to those fat red enemies with spears and either a wooden or metal shield). Hate them mainly because of their ridiculously high HP. On my first playthrough, I landed ~12 hits with my sword on the one that is on a bridge high inside the great tree in Faron Woods and he still wouldn't die! Instead he hit me once and I fell down to the bottom of the tree and had to walk all the way up again
And of course this was only the weaker variant with the wooden shield. Seriously, how man sword hits does he take before going down? 16? 24? Over 9000? I never tried to finish them with my sword ever again after that, it's just a waste of time. On my current Hero Mode playthrough, I played it safe and bombed him to death (took 4 bombs IIRC).
Their high HP also annoyed me during the escort mission I already mentioned above. You must know, arrows are the key to getting through that part of the game. So the wooden shielded one takes five regular arrows to go down and the metal shielded one a whopping TEN arrows! But you only have 20 arrows max. normally and supplies are sparse in that region. Needless to say I ran out of arrows near the end of that section and ran into a situation with two Bokoblin archers and one fat spear guy. Also needless to say that I failed horribly. And if you fail there and the guy you have to escort gets hit around 3 times, you have to start the WHOLE DAMN section over again! So I went back to upgrade my bow to the Sacred(?) Bow (the level 3 one) and bought a quiver which I also upgraded to level 3 so that I could hold 35 arrows, only this way could I make it through that section easily.
But enough with the ranting, the boss battles were really fun and unique and made up for some of the annoying regular enemies.