Certainly an interesting list. Had more games that I've played than I expected .
Major Disagreements:
Mario with 4 out of the top 5. I like all of the games included in that list, but none of them are Top 5 material
OoT as #1, but this seems to be a complaint I could file against a good chunk of best game of all time lists. Personally, if it's Zelda, I think both Wind Waker and Majora's Mask do a much better job of atmosphere building and weaving an interesting narrative.
There is absolutely no way that anything to do with Final Fantasy 13 deserves a spot on any best of list.
Twilight Princess at #10. TP has a good atmosphere, but the narrative goes all over the place, and the game gets dragged out into an utter grind towards the end when you're just bouncing from dungeon to dungeon to find all the mirror shards. Plus they ruined Zant at the end.
Kinda sad that nothing from Devil May Cry made the list
Major Agreements
...by the same token, I was happy to see Majora's Mask and Wind Waker both on this list (and fairly high up as well)
Glad that Okami and two of the Ace Attorney titles made it as well. Both underplayed gems from Capcom
Wonderful 101 got some love too. Another underplayed gem, this one from Platinum
All of the Metroid games on this list were ones that I would've included, with the exception of swapping out Zero Mission for the original.