I disliked the portrayal of Beorn. I really, really disliked that there was no enchanted stream and the Mirkwood part was way too short. Not to mention it was Elves who rescued the Dwarves not Bilbo. But the overall "no food, no hope, no light, no air" etc part from our very own HotW was portrayed nicely.
I really don't understand how can a group of orcs can get that close into Elven territory either, nor into the Lake-Town. If orcs could enter like that easily, Bolg with warg and Legolas with his horse, why can't the dwarves enter too? Why pay all that money in the first place to smuggle themselves

I hate, hate, hate the love triangle. Also Legolas should have had only a cameo and a part in the battle in the 3rd film that's it. He had nearly more screentime than Bilbo! And why even include a scene about Thranduil's face? What is that? An illusion spell? Why???
But the worst part for me was the Smaug and dwarves chasing part. I got so bored...
Do not let me even start on Gandalf vs Sauron magic duel thingy.

All in all when I look back to this trilogy I will only be glad of the new soundtrack and new GW miniatures. Also I think it helped Cubicle to produce the TOR game or motivated them and to put it in the Rhovanion region. So whatever. This trilogy cannot even come close to LOTR movies.