It has nothing to do with your brand of GPU. This game has a bloom effect that does not work well when you increase the internal resolution. It's been that way for ages in Dolphin. Blame Nintendo.
You can disable the bloom entirely with AR codes. See here: http://www.gc-forever.com/forums/viewtopic.php?f=38&t=2472
You can disable the bloom entirely with AR codes. See here: http://www.gc-forever.com/forums/viewtopic.php?f=38&t=2472