Nice rant, but you are wrong with your assumption that players are stuck in a Nintendo bubble. The reason Nintendo games end up on top is that they are fewer, but of constant quality. What I mean with fewer: many people here had Final Fantasies on their lists. But there are 15 or so Final Fantasies, which is splitting the votes. Yet there are few Nintendo games all are agreeing are great.
I mean look at the separate lists from the people: http://gamrconnect.vgchartz.com/thread.php?id=241290
Can you see so much Nintendo dominance in the single lists? I guess not. Sure, there are a few that have lists consisting mostly of Nintendo games, but at the same time you have others that have only or mostly PS in their platform column. That the end result is different is because everyone mostly agrees on the Nintendo games while from other devs and on other platforms very different games are picked.
Reality has a Nintendo bias and VGC's list reflects that.
Another point of view is the simple question which game publishers could carry a console on their own. With the only reasonable answer being Nintendo - as they are the only company that a large enough number of people would buy a console for - it makes sense that Nintendo occupies so many of the top spots while other game makers are more scattered across the list.