Just finished my thief play-through, a lot of people complained about the game's difficulty (i.e. being too easy) but 3-squad dire bears/dire wolves really did give me quite a bit of trouble, as did some boss fights (alien one, al gore, 1-2 more that i can't remember). Most normal encounters do become banal after the first 2 levels though.
Haven't finished the game but I've had some trouble with fights as well. If you screw up the QTE stuff you lose. I'm playing on hardcore though and with a fighter. Had trouble with a random fight at beginning of the game. After losing 3-5 times it just disappeared. Not sure if they did that purposely because I lost so much.
The QTE stuff sucks balls. Here you have all these amazing abilities and you're stuck staring at a white circle around your character instead of watching them. I will never understand why QTEs became so big. You get these cutscenes where your character does something awesome and instead of watching the scene, you're watching the edge of the screen or wherever the keys show up and not watching the scene itself. It makes no sense. Your character can also be covered up so you can't do the QTE properly when attacking because an enemy is in front of them, which is what happened when in the Al Gore fight.
Didn't have much problem with the aliens. The baseball bat skill really helps with them. Although I did die to the boss. If the pilot gets low on hp he promotes the co-pilot to pilot and runs away. The co-pilot then proceeded to get 2 turns in a row and the second turn did a lot of damage killing me. Didn't let that happen a second time but thought it was interesting.
Al Gore was a huge pain in the ass. I had to use a few speed potions to get several turns in a row to defeat him and his secret service. Fight was tough and I kept getting bad rolls with Professor Chaos ability. Plus it was just impossible to block the assault rifle fire. Manbearpig was easy to beat though.
I'm only on the Goth kid quest now. So maybe I was just too weak for the stuff I was doing.