I think the enemies for me got more annoying and difficult starting in Aquila. Like what some people have already said, the Stymphalian birds were a nuisance, especially when you had to fight 16 in order to get 4 incense. Harpies were obnoxious, especially how often they were able to critical on my privateer. The sillento fish in Valencia pt. 2 were terrible; it was rare when I went a fight without having one of my companions die. The Duomo guards were relatively easy on me when I did it on my swashbuckler, only had two companions die during the entire dungeon. But my least favorite enemy has to be the satyrs. Little devils they were...
From my memory, the worst ones were the following in no particular order:
Manticores: Relentless triggers way too often, enough said.
Valencia II enemies with Assassin's strike: Assassin's strike for a NORMAL enemy? The crits were RIDICULOUS. Challenge is good, but THAT is just BULL! Back Stab would've been fine, but Assassin's Strike? Really?
I'd file a chunk of Valencia II's enemies here. They have insanely powerful crits and some of them having powers made this pretty annoying.
Debatably bad (I didn't have as much trouble as some of you did with these):
Satyrs: They have Improved Mojo Blast 2, so the easiest way to deal with that is to spread out a little by making sure that NO ONE is standing right next to ANYONE. Other than that, these guys aren't so tough.
Stymphalian birds: My experience with them varied from pirate to pirate. Some did well, some didn't. I'd get rid of the "ravenous" ones first, since they have Relentless.
Harpies: As long as you avoid using melee (and/or raise your defenses if you MUST use melee), you should be fine, just mind the occasional critical.
In all honesty, most Aquilan enemies I'd file under "debatably bad" from my experience.
This, however, is part of the fun of Pirate101; the combat is NOT predictable! You could fight the same enemies and wreck them one time or get your rear handed to you the next! It all takes practice and strategy, it can be done. :)