Ikuta is a long way from "downtown". You could take the train into Tokyo (but don't even think of riding trains in rush hour with a stroller).

Fold down changing tables are fairly common in public restrooms in department stores, stations etc. You should expect to carry your own supplies of EVERYTHING. (That's right. Don't expect toilet paper, hot water, or hand towels to be available). Some restroom facilities are 21st century and some are straight out of the middle-ages. You get a "nose" for the good ones fairly quickly...

Tokyo toilets:
http://www.travelwithyourkids.com/de.../tokyo-toilets

Sites like these have some valuable information:
http://www.tokyowithkids.com/
http://www.tokyoessentials.com/kids.html
http://www.travelwithyourkids.com/de...ps-for-parents

In terms of expectations, I think a young toddler can get away without any knowledge of Japanese ettiquette. You will be expected to remove his shoes in "shoes off" areas etc.