AC would be on the top of my list, although the only game that I might like better is Disaster: Day Of Crisis. Of course, this game could be a total flop for all we know. And AC could be a masterpiece. But they definitely underestimated AC, even from a POV that isn't bias. Let me just point out the fact that NP gave AC #19 of ALL GCN games and ACWW #19 of ALL DS games.
If I were to make a list like that, I'd put Mario Super Sluggers at the top. The other games really don't appeal to me. But if I was forced to choose two others, then I'd pick Wii Love Golf and Wario Land.
I actually agree with the #1 game. Fatal Frame is being published by Nintendo, developed by Tecmo and directed by Suda51. Amazing combination if you ask me.
Rune Factory is too high.
Fragile would be #2 for me.
AC Wii and Samba De Amigo should also be higher.
etc
Edit - Also, I understand the author's reasoning for not including Mad World and The Conduit, but the former in particular definitely deserves to be on the list.