I'm 3 weeks into my 5 week trip and I have Done Tokyo and Osaka.
I have been primarily looking at G1 toys and any printed materials and I can basically reiterate what everyone else has said;
For Tokyo - if you want tonnage just go to Nakano Broadway and the Mandarake/other stores there. There is either too little quantity, or what is available is of lesser quality in any other location including Akihabara.
For Osaka - Mandarake Grand Chaos is a good place for G1 (Mandarake Umeda is just for Manga, although there are a few Transformers Generations books there), as is Hero Gangu in Den Den Town. I did not go to Jungle as I was just too mentally overwhelmed and I have since left the city.
Pictures available on request.