Whopper is the better "burger" if you're looking for a traditional hamburger. Though if you're really looking for that, you may as well go with more upscale choices.
Big Mac is the more unique burger. It just has a taste, like it or not, that is different. It's not everyone's thing, but for those who like it, nothing quite hits that spot when you want to have a Big Mac, you need to get a Big Mac.
So I guess in a weird way, even though the Whopper is probably the better "burger", the Big Mac is the better "flagship" or iconic sandwich because it's very specific to McDonalds (like it or loathe it).