I went here on Saturday and it's totally a disappointment. If you're gonna be in Ikebukuro, then it's on the bottom floor of the Seibu located in Ikebukuro station. It's a tiny little stand and they only sold 3 flavors, sakura green tea, red chili and sublime (I think this was some kind of bitter chocolate one and it was limited to 300 units per day). There was a special sweet bean paste sandwich flavor if you spent more than 4200 yen. Once that was gone they switched to strawberry, which is pretty readily available. You'll honestly find more variety in Kit Kats at regular candy shops. The best one I've found is in Odaiba at Diver City (though I can't remember the name at the moment).
Here's some pics.
I'm sure it will get better, but right now it's not really the Kit Kat Mecca I had pictured =(
Still, if you're in Ikebukuro, you can eat some made delicious ramen at Mutekiya which is really close to the station. It's hands down some of the best ramen in Tokyo (opinions on ramen differ obviously), and check out Sunshine City.
Here's the outside of Mutekiya for reference.
Also, for all that is sacred listen to this man
Damn it! Oh well while you are our "man on the ground", let us know any other delicious shops and eats on your travels that are hard to spot unless you've been there please! a lot of us are going in the next few months so it would be appreciated,