Well, the hardest one for me is either the Hydra, Diskylos, or Antinous. However, Rooke is also pretty difficult for a musketeer like me, and so is Bishop. (Little hint here: Use an accuracy decreasing move on Bishop in both of his fights so that way his spells never land. For me, I use Goronado and his Vicious Charge. With Rooke, ALL Swashbuckler team. Use El Toro definitely, and another 2 Swashes of your choice.
As far as I have gotten in the game, I would say the hardest enemies are the clay warriors in what's-his-name's tomb in the Paths of Penance, right before you fight Moo Manchu. In close second comes Captain Blood, and third would be Deacon. I also highly disliked the scorpions in Cool Ranch. Chumba Wumba is a nightmare for Witchdoctors. Well, that's all I can think of for now!
Based on my experience so far the top 6 hardest enemies not counting bosses are.
1.Stayar-( I don't know the exact spelling ) What can be more challenging,to defeat a none boss then these creatures ? In my opinon,these are by far the most powerful none boss fight I have ever encountered. ( I was helping a friend.) ( Aquila )
2.Bone Drake- A real pain if you ran into these,while first entering Valencia.But they get easier by the time,your pirate(s) pass the level 50 mark... um.. i mean cap .( Arvanus sky way )
3.Harpies- These are though Beasties,I have came across. While Battling them in the Achaean sky way,even for a max leveled pirate like my Buccaneer. They take a while to defeat, and they hit hard. ( Aquila )
4.Dragon Clockworks-Familiar ? If you stick around during tutorial, Mr.Grady I hope this answered your question.These are one heck of a battle espically if you are a musketeer.Force to reckon with if you got a shooty weapon.( Marlyebone )
5.Terra Cotta Warrior- This clay figures are down right nasty,with first strikes and relentless these are one of the most powerful enemies I have encountered in Moo Shu. ( Moo Shu )
6.Striped Buffaloon- You thought those durngo version are though,these are tougher still to beat. Got to train long and hard to challenge these creatures. ( Cool Ranch )
There you have it the dirty half dozen, 6 of the most difficult beastiies to defeat in my opinon.