Just saw the itinerary. Few cents' worth of opinion:
1. Day 1 seems a little ambitious, no? I think it's more realistic to have 3-4 places to visit. And in Kyoto you can also visit Nishiki Market.
2. Day 6 - by the time you do Omotesando, I think it's easily 4-5pm, unless the first 3 places you're doing touch-n-go style. Suggestion is to pack lunch (i.e. bento from Family Mart/ 7-11) and enjoy a nice picnic at Yoyogi Park.
3. Day 7 is interesting. You're doing it the other way round vs mine
What i did before was Asakusa-Hamarikyu-Tsukiji-Imperial Palace-Tokyo Station. We board the Water Taxi from Asakusa in the morning and got down at Hamarikyu Garden. The rest of it we walked from one place to another, because they're within walking distance.
It's a pretty touristy thing to do, but I really enjoyed it. I don't mind riding it again when I'm back in Tokyo haha. I think your "boat trip" is in reference to this.
http://www.gotokyo.org/en/tourists/info/access/access5.html 4. Day 10 - I suggest you push Shinjuku Gyoen to the morning/ afternoon. In winter, it gets dark early, ie. 4-5pm sometimes feels like 7-8pm. So if you go in the evening, I should think it's less enjoyable compared to the earlier time. Secondly, is there anything to see in Winter? Back in Autumn, I went there to see the autumn foliage it was really beautiful. Not so sure about winter, you may want to check online first.
5. Suggestion: do Ginza on Saturday/ Sunday. Pedestrian's Heaven is over the weekend from 12 noon onwards at Chuo Dori, Ginza.
Not sure bout Osaka, but in Tokyo you can get the Metro Subway Pass, more value for the 3 days pass. However you'll need to have good planning to fully utilize the pass. It can potentially save up to few times of your transport cost over 3 days.
http://www.tokyometro.jp/en/ticket/value/travel/ For example if you're going Akihabara, usually you'll search to Akiharaba station. However that station is under JR Line, so you can't use the Metro pass.
But, you can always stop at Suehirocho station via Metro line. It brings you directly to Akihabara as well - but this is not a well known fact among tourists especially first few timers. Need to do more research if you want to utilize the pass.
Thanks for the tips @sweet_pez! Will try to follow as per ur suggestion for our Tokyo trip.
For our trip in Osaka and Kyoto, it is not finalized yet as we are still keeping our options open whether to head to kyoto 1st then only come back to Osaka for 2 nights or maintained as it is.
we are also thinking whether to drop by Kobe if there's enough time (which I doubt it), anyone know whether its worth to go there based on our travelling schedule? fyi, me and my partner are not really into beef meat, so if there's nothing much other than trying the beef there then might as well we'll just skip it.