Flaws make a fictional character engaging, but the flaws on a representational character can be easily perceived as a comment on the the whole group. If Wyll had a more complex personality, people like the OP would point out the supposed racism behind the darker parts. For reasons of safety (white) writers will create dull goody personalities for PoC characters.
Lots of good points, but I think this part becomes more difficult to avoid when the game only has one black origin character/companion. Regardless of the devs' intentions, he kind of becomes the representative for how they choose to portray black main characters. If the game had six black characters with backgrounds and story lines then I don't think anyone would think it was racist if each of them had different negative traits and complex personalities. On the other hand, making the one white guy a paragon of virtue in such a scenario might be interpreted differently

Wyll's original EA concept was much darker, and people complained he was too bland all the same. Wyll was motivated not only by heroism, but also revenge, to the point where he was willing to make evil choices to get what he needed (torture the prisoner in goblin camp to obtain information). Same goes for his father, there was a dialogue where he hinted at the duke being not such a good person either. Larian chose to change his character concept last minute, though they left some of his old questline (Mizora being trapped in moonrise towers and needing a rescue).
I don't recall people commenting about his EA characterization being racist, though obviously it is possible there was feedback like this, as only Larian would know about it. The complaints that I have seen were that he was bland, despite that he had very obvious flaws. But for me this is not about his characterization, it is about the amount of content and focus on Mizora (and in last quest to emperor), and how she is handled in the game.
That said, there is also some Astarion writing I find problematic, but I have lost much interest in discussing that character.