I don't know who is the smartest between Fred and Willow! But I think Fred is smarter than Willow and even Giles! Don't get me wrong Willow is one smart, powerful witch! But Fred knows how to open portals without witchcraft, I'm pretty sure!

Fred followed by Willow. I chose Fred over Willow because while Willow was exceptionally smart for school level, Fred was studying a degree in physics. We didn't see what Willow was planning on studying at college (did she drop out too, like Buffy? I can't remember much mention of anyone's college life after season 4).