I have found the price of each weapon to make no sense -- sometimes I am receiving less money than the weapon itself costs! (ex either the Great Hammer or the Great Sword sold for only $28, but the ingots alone cost $30!)
I found it annoying that you had to hammer a medium-sized blade 4-5 times to get the equivalent hammer style (yet for the Great Sword is varies on the first hit).
I found the controls clumsy and annoying. After a while I got the hang of it, but it was still much slower than would have been nice. With pieces flying around when you let objects collide strangely (due to no depth perception), I found myself having to pick up objects several times (sometimes), put them on the table, and try to combine them again. (Very frustrating!)
After levelling up a couple times and putting each point into Charisma for more money, I wasn't at all sure that I was getting better deals.
It's annoying that some customers will say "too slow" even if you give them a weapon within seconds (ex because you premade it)
When I finally got enough wealth so as to be able to afford Tin Ingots, I sold a Tin dagger for $112. But the Tin Ingot was $100 and the Fancy Hold was $5! A mere profit of $7? What's the point of Tin over Copper?