I feel like there's a lot of strange assumptions being thrown around about the demographics of the people who responded to this poll, especially for those people who voted for Nintendo titles. I can certainly understand that to a certain extent these assumptions may even be true, but it hardly seems helpful or relevant when a large majority of people agree that those Nintendo games are the best games of all-time.
Would this list be more interesting if it included choices like Master of Orion 2, Katamari Damacy, Meteos, or Bushido Blade (all of which are in my personal top 20, but not top 10)? Absolutely. But, I'm not going to put Drill Dozer in my top 10 ahead of Super Mario World just to have a different 2D platformer that's more niche.
I'm 29 years old now, and I've been pretty serious about gaming for 23 of those years. I've played thousands of games, but the fact remains that Mario and Zelda really are that damn good.
If you want to have a "best games of all-time" list that excludes the best games of all time it just seems sort of pointless. Also, I don't think your list would end up looking too much different if you decided to do a judges' panel type list. Sure you would have less entries from single franchises but that wouldn't change the overall look of the list too much. And that would be the result of a conscious decision to mold the list, not necessarily because your imaginary council would think that Wind Waker isn't good enough to be in the top 50.