in my theory, Giygas went back in time and tried to destroy ninten's family lineage. but still he got born. but since there was some changes in the past, he wasn't born as early he was born later, as Ness instead of Ninten. that's my theory and i'm sticking with it. it took several years to formulate. but I like it.
but it's just my theory, you're all free to make up your own of course. so says Itoi
(he more or less encourages you to make up your own reasons)