Shinjuku is at the top of my list right now for the exact reasons you mentioned. Plus I really want to stay somewhere up high with a good city view. It also might be nice to stay somewhere with a view of the Imperial Palace though. Navigating the Subway system is going to be interesting with a stroller, as I just found out that most stations don't have an elevator. With a one and three year old it just isn't optional though.
I am so glad I've started researching so early because there really is so much to plan. I just got my Lonely Planet guide, but haven't even had a chance to crack it open. I have been reading my Just Enough Japanese book that I bought at Epcot last year, however. Not that I remember anything though.
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And now Harry, let us step into the night and pursue that flighty temptress, adventure! - Albus Dumbledore
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