For what it's worth, Best Game and Best d20 are separate categories, and I'm not entirely certain that D&D will be eligible for the same category as BRP.
Also, the judges are recruited from a variety of places, not just ENWorld. When I was a judge I came from RPGnet, and I think that on my year at least we had a good selection of non-d20 stuff.
Still, I can understand the concern. While the nominees are selected by judges who review all the material, it's up to a fan vote to see who wins, and WotC has an aweful lot of strength in that category. I think this year might be a decent gauge of how that translates into actual awards, with Star Wars Saga in the running, but I think mostly we'll just have to wait and see.
Still, I'd hate to see BRP not get some of the recognition it derves. It's extremely well done.