Amazing work Leadified.
Shame the results themselves weren't more interesting. 6 of the top 50 are Pokemon games (like, seriously? I love me some Pokemon but is there really any justification for having anything besides Red/Blue and any one of the modern entries in the top 50?), 5 are Final Fantasy, 8 are Zelda, and 7 are Mario platformers. zzzzz
Um Yes, yes there is. Red and blue aren't the best pokemon games, quite frankly I'm happy to see so many pokemon games in the top 50. I'd rather a mystery dungeon game (time/darkness/sky) be there instead of platinum and gen 4, but the others definitely deserve it. Especially GSC, easily the best Pokemon games, easily.
Hence why I said Red/Blue and one of the modern ones. Red/Blue because they were the first, the innovators, and the basis for all of the subsequent entries, and therefore I'd argue the best for their time. And one of the modern entries - whichever is generally considered 'the best' at the time of voting.
If you think 12% of the absolute best games of all time are Pokemon games then at least you're guaranteed a new top 50 game every other year or so, so there's that.