I used to live in japan so not up to the latest stuff, but heres my suggestion.
I did my advanced through Guam Tropical Dive station (GTDS), good well organised set up and a nice boat, lot of the milatary seem to dive with them as well. The course should only take 2 or 3 days. Get them to book a hotel for you as well, the owner is in with the local tourist board. We stayed a couple of nights in a cheapy hotel near their shop, then chilled for a few days and they got us a good rate at the Hilton (Hilton tried to up the rate which i was ok with, but GTDS had another word with them and it came down again)
If you are interested in a bit of wreck experience you could dive the Tokai Maru / Cormorant as part of the training (no penetration of course) These two ships are lieing hull to hull in the harbour and can be done in one dive, Tokai is Japanese freighter from WW2 and Cormorant from WW1 neat huh.
If your comfortable and want more wrecks then plan another trip to Truk. Japan is one of the easiest places to access Truk, Yap and Palau from, wish i had done some more trips there, if you dont go you will regret it later