I agree that there are problems with Wyll, and that (at least partly) these are related to his race. Despite him getting the most interesting class, his personality is kinda boring. He feels like the most generic fantasy good guy with zero depth and complexity. As also seen in many recent movies or series, characters who "bear the burden of representation" tend to be portrayed as strong but boring people. They can't have any interesting flaws or quirks, because that would jeopardize their role as "inspirational representation". 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.
Another issue with Wyll from a gameplay perspective is that he fits the same role as Gale, whom you most likely meet earlier. Gale as a more generic wizard also seems like a safer bet, especially on a first run. This alone puts Wyll into a tough spot. If he was a paladin he would be more popular, and thus getting more attention from Larian. There is no need to look for any racism here. Especially the outright hostile racism OP seems to cry about.
