@deathly_hallows Not that consoles are more popular than handhelds, but that the biggest console games tend to be more popular than the biggest handheld games. Check out our past winners:
2012: Console - Xenoblade Chronicles, Handheld - Kid Icarus: Uprising
2011: Console - Zelda Skyward Sword, Handheld - Super Mario 3D Land
2010: Console - Super Mario Galaxy 2, Handheld - Dragon Quest IX
2009: Console - New Super Mario Bros. Wii, Handheld - Mario & Luigi: Bowser's Inside Story
2008: Console - Super Smash Bros. Brawl, Handheld - Professor Layton and the Curious Village
Which of those handheld games would have really stood a chance? I can't say for sure, but I suspect the console games would have taken it 5 years straight.
The other thing that was fueling the decision to keep them separate is that a lot of people simply don't own both platforms. Especially right now with the Wii U still being relatively new and many still holding off on it, I'd bet that we have like twice as many 3DS owners as Wii U owners here. And since our GOTY voting is basically a popular vote, that gives an unfair advantage to games on the platforms that people own most (a huge issue with the way a lot of multiconsole sites do their GOTY stuff too, but they tend to not do user voting either.) Not everyone has played every game up there of course, but if they own the platform for any given category they at least had access to every game in it.
Of course, that was an issue when we combined "consoles" and "handhelds" last year, for instance a lot of people had the Wii but did not have the Wii U yet. Something that I thought about when combining, and it might have helped give Xenoblade Chronicles a bit of a boost. Tough to completely avoid these issues, but I think there are enough distinct console and handheld gamers on this site that smashing them together in voting would lead to an end result highly skewed by the platforms people actually own and / or have access to.