I was there (Akihabara store) in late november and didn't see any of the Specialist sets there but their products change so quickly you never know what goodies you'll find. They did have quite a bit of henkei stuff though.
On the top floor there are a couple of areas of Transformers so don't just look at the glorious goodness behind the glass cases... check out the WHOLE floor to find bit and pieces. Last time I was there they even had loose figures in plastic bags hanging on a display near the cashier too. Just don't pull out your phone or camera to take photos (or don't get caught) as they get REALLY stroppy and follow you around to stop you.
There is also a store on the street where you exit the train station heading in the direction of Manadrake on one of the corners of the first main road you come to that also has Transformers. Again - find the lift and jump on up to their (I think) top floor but look at the guide for the "robot" floor. The prices are inflated (compared to what I pay in HK) but they did have a good selection of boxed sets and recent MP's. Their ground floor is glass cabinets with figures from every anime/manga/mecha you can think of ... and again... no photos allowed but really nice to walk through.