Hmmm... I'm coming to this thread a bit late but there were a couple things said that I would take minor issue with.

I have a 4-yr-old in Japanese day care and a 2nd-grader in Japanese Elementary. I don't see any signs of them being treated any differently than other kids (except that the girls all seem to like my older son). The 2nd-grade class has done some pretty interesting things that, when I went to school, weren't even on the curriculum. Most of the pressure on kids comes from the parents who want their kids to enter Todai someday. From what I can tell, things don't seem to get tough until around middle-school.

If you're going to be here a while and are thinking International School, though, your relocation should take that into account. There aren't all that many International Schools around and transportation can be a challenge if you have to commute to take the kid to school and go back the other way to get to work.

Also, there are no problems with diapers or other baby supplies, as kids are kids and some need diapers longer than others.

I would definitely not recommend Roppongi if you have a toddler. You will want an area with parks to play in, streets on which a kid can safely walk and ride their bicycle, and at least a bit of quiet on the weekends (when there's no election coming up). How close is your office to Tokyo station (Chiyoda-ku is pretty big)? Try Nakano. I commuted from Nakano to Oimachi (near Shinagawa) for years. I'm lucky enough now to have a job where I can work mostly from home but I still go to the office now and again and there are only a few windows of time during the morning commute that I would feel qualify as "crowded" -- maybe I'm just getting used to it. Anyway, Tokyo to Nakano is a straight shot (one train, no transfers) and it only takes about 20 mins.

I have heard that trains in the other direction (ie: Chiba) are very crowded. Also going West from where I'm at it gets a worse. Maybe I'm just lucky.

BTW, there is no subway from Ikebukuro to Shinjuku and very few from which one can see trees. The Yamanote-sen runs between those two stations but it's only about 4 stops and less than 10 mins total. On the West side of town, there are a number of train lines that can put you in reasonably suburban surroundings within a half-hour. Unfortunately, fewer choices from the East side (Chiyoda-ku) because the bay is kinda in the way. But you can get down to Kawasaki in less than 20 mins (assuming Tokyo as the starting point) and things are less crowded and less expensive down there.