When you enter the ground floor, you will find more generic Square toy. The 2nd floor which is really a mezzanine is where you will find all the Final Fantasy and Kingdom Hearts goods. It was a little smaller than I expected but it had the figurines, jewellery, posters, models etc...
The first thing you see when you head up the 2nd floor is the costume for Genesis. I think this is the one that he was wearing in Dirge of Cerberus. Very imressive. If I am not mistaken the muse for Tesuya Nomura was the Japanese rock singer Gackt who actually wore this in one of his videos - Redemption (see below).
Gackt - Redemption Vid (Click here)
The most impressive feature of the store is the model of Sephiroth on the floor. It is built into the floor with a glass casing so you can peer down into the the 'chamber'. He is in stasis... in a similar position to when Cloud went to give him the Black Materia at the Northern Crater in the game Final Fantasy Vll. This version of Sephiroth is also known as Bizarro Sephiroth (If I am not mistaken) where his body from below the torso is covered by his Single Black Wing. Hence he is also known as the One Winged Angel. The detail is amazing. He is so lifelike that you can imagine him opening his eyes at any moment and giving you his evil grin.
The figurines were a little limited. The pictures below show what they had. For Final Fantasy Advent Children, they carried Yufie, Vincent, Reno, Sephiroth and Kadaj. There were also Final Fantasy X figurines, of note Judge Magister Gabranth was available. There were 6 posters for sale, a little limited in choice IMHO. I was a bit disappointd that the Play Arts, Cloud Strife figure not available. In fact I couldn't find Cloud anywhere. The stores in Akihabara stocked the same figurines. I saw a Tifa there but it was a display model only.
Yamashiroya (huge toy store)in Ueno had a big display of Final Fantasy Crisis Core (they just launched in September) with posters at the front of the store. One of their front windows were dedicated to FFVll stuff. However, they had the 1/4 scale Masterpiece Arts Cloud Strife in the window. It was very well done, the detailing was amazing, if you want it you have to order it. Retainling for 47,000 yen.
In the end, I bought the Sephiroth and Kadaj figurines. Very happy with them. The pricing was pretty much the same in Akihabara, although I did find 1 store that had it a litle bit cheaper. But if you've gone all the way there, might as well buy something from the Square Enix store.