Not bugs, but rather peeves that makes the game seem a bit too linear:
Skill books: Why do merchants only have a set type of skill books in each area? They are linked to player level and price, so why can't players buy for instance Cloak And Dagger or Barrage in Cyseal? That's a bit like a book shop only selling school books for first graders. "You want a thriller? Well, in this shop we only sell Tom Clancy novels."
Items: Same thing as above. You can't use a high-level item effectively, because they're linked to level. Very good idea. So why do you still only find rubbish at the beginning of the game, despite maybe having invested a lot of skill points in Luck? The whole loot system seems to be broken. Also, I'm on my third playthrough of the EE, and the rings, helmets and medallions I find are uniformly crap. If I find any. Max two minor enchantments, and they often make no sense: I found a plate helmet that gave +1 Bow and +1 Shield Specialist. Who's gonna wear that? A Blue arbalest with a whopping 189 base damage, 11-18 Earth damage, and a point in Single Handed. With a level 15 to use. WTF? Meanwhile you find a Legendary bow with 60 max damage and no other enchantments. Why do you find Epic or Legendary items that has the same minor stats as blue/Uncommon ones? What's the point? I have also previously mentioned the cloning issue, where you find similar items in a small area. By the time I finished level 6 in my current playthrough, I was selling off Green sarongs giving +2 Initiative by the truckload, and had close to 50 knockdown arrows. Item generation seems to be completely out of whack.
Adventure Kits: You can only complete the Adventure Kit weapons late in the game, by which time they're pretty much useless compared to what you've already got. Also, there are no in-game clues to where you find the various parts, which could have been nice mini-quests. The whole thing seems redundant and frustrating to me.
Crafting: I think many people here have pointed out that the crafting skill seems to be broken. Even a level 5 craftsman can't create top-notch items with multiple enchantements, like different types of damage. Shouldn't a level 5 crafter be able to give a better output than a level 3? Like additional elemental damage? Debuff potions are pointless, and there only seems to be one of items like Joshua's Spice or Scope in the entire game. Shouldn't we be able to craft those on a high level? Many recipies don't work like they used to, and certain kinds of items can't be enchanted anymore, at all.
Skills: Is level 5 really the maximum skill level? Does this mean that if I want to invest all skill points to make a master Pyromancer, I can't do so? Why impose such a limit on skills? It makes no sense from a roleplaying perspective, as long as you only get a certain amount of skill points throughout the game. You can buff weapon skills or stuff like Telekinesis with items, but so far I haven't found a single item that buffs for instance Scoundrel. That's just weird.
All in all it seems to me that the Enhanced Edition has taken quite a few steps towards being more linear, and away from the freedom that was the selling point of the original. A lot of things have been improved, but imposing nonsensical limitations on character development and basic functions, is a bit of a downer. It may make sense from a balancing perspective, but I would never tell my P&P players that they can't use their Experience Points to create the character they want. If you want to play a blind mage with low movement, but genious level intelligence, then please do so. When you tell me that my mage can't have more that two Master level spells despite putting all points into that skill, that severly limits my experience of the game.
Just my thoughts. This is still my fave CRPG, and I've played through the original over 10 times. I just expected more, not less, of an Enhanced Edition.
