Probably, nostalgia is a powerful thing. Personally, the VF-1 is my second favourite Valkyrie (next to the VF-4 Lightning III), and I don't even know if it's because it's really such a great design, or just because it was the first. I mean, it definitely is a great design, but so are the YF-19, the VF-11, and many other Valkyries.
It probably helps that I was always a huge fan of the F-14 and the F-15, and the VF-1 bares a strong resemblance to both.
I think its all due to the awesomeness of the VF-1... If the show had started with like the 19 or something, it would not have been as popular.