im surprised so many here agree, and even more suprised that they think SM64 aged poorly

Having played both recently (on my N64, duh) I have to disagree. SM64 still plays very well, and even though the graphics aren't as technically good as Bajo, the art style has held up better to my eyes.

Banjo was certainly the most in-depth game, but SM64 was/is more fun to play.

Haven't played them, but seems like a normal opinion, not sure why they call it controversial. Both games look great for their time. Personally I can't stand N64/PS1 graphics though. Visually I would probably give the edge to Banjo-Kazooie. Platforming is probably Mario, but what do I know.

That's the part I find odd. Other than the way it looks SM64 hasn't really aged at all. I played it for a bit a few weeks ago for the first time in years, and I was able to pick it right up and play it as if I'd never stopped. It was great, actually haha!

I think they are both overrated and only called great today because of nostalgia

I doubt MS has anything to do with this. Like I said before, this is not exactly a controversial opinion!

It has certainly aged better imo.

I really enjoyed Donkey Kong 64. Most people I know did. The only people that I know that do not like the game, are people I have just happened to stumble upon via the internet. 
Although I will admit that the beaver minigame was a hellish endeavour. Very rage inducing indeed.

That being said, I agree that Polygon tries its hardest at being controversial. They probably like being edgy or something along those lines.

Or because they defined the leap to 3d gaming.  I guess that might not seem important if you were born into 3d gaming.

Banjo Kazooie was just an all around better game. One thing not really brought up is how awesome the level design in BK64 was.