To add to this discussion, I will talk about the areas that I personally struggled with (and in some cases am still a little hazy).To be clear I own Fantasy Hero Complete, I purchased the PDF from here.
* Damage Class. I read about Killing Damage and Normal Damage and resistances to that damage (physical defenses against Normal Damage, resistant defenses against Killing Damage). That wasn't too hard to grasp. But as some point in the book it started talking about DCs and seemed to skip the process of converting from DC -> Killing or Normal Damage (1DC = 1D6 Normal Damage, 1DC ~= 1/3 D6 but not really...; or 3DC = 1D6 Killing Damage if I remember correctly). I actually didn't figure that out, assuming I have it right, until searching the forums and reading about other people asking about it.
* Calculating the cost of powers. This was a big one, the rules in FHC do not seem very clear in many cases. Active Points = ( Base + Adders ) x (1 + total of add advantages ); Real Points = Active Points / (1 + total of all limitations). Now figuring out exactly what the Adders, Advantages and Limitations are turned out to be more tricky than I would have expected. To compound the problem the formula isn't super easy to find, even when I knew where to look.
Honestly that's it for me. Combat seems clear, its a bit different from Gurps - mainly in the way turn order occurs and how speed is handled - but its not bad. It seems to me that Damage types and Powers are so critical to the system that the book needs a lot more examples and it really needs to make the wording itself much clearer.
That said I am going to use the system for my next campaign because I wind up building the world, culture and customizing the system for my games anyway - with Hero that customization is really emphasized. So my criticisms are not towards the system itself but rather the documentation.