Yeesh. A lot to go through. First though, you can use your Icoca card in Tokyo. There is no swapping it for a Suica.
Your Day 2 looks pretty jam packed. It's hard to say how much time you want to spend at Denden Town, Shinsaibashi, etc. Namba Parks can be skipped - great for the Christmas lights, but unless there is some store there you want to see... Some places won't take long at all. America-mura can be skipped as well. But if not, you'll be through it very quickly, unless you want to go shopping for jeans or something. Hozenji Temple is small, and close to Dotonbori. Shinsekai, like Dotonbori, is best in the evening. If you are only interested in walking through the Kurumon Ichiba to see it, then you might have time to go through the Sennichimae Doguyasuji Shotengai which is close by - they specialize in cutlery, but there are many stores with a wide variety of stuff, all done in Osaka's unique methods of wild color and display.
You'll be too late to see any roses at Nakanoshima if that was your desire. There are some events on weekends you could see, and it is a place to chill out a while if you like. Or skip it if time is short. You might find that you are spending a lot of time running around to all the places you mention. There is not much happening in Nara at night, so if you find yourself falling behind in the previous days, you could see some places in Osaka after Nara, if you like, and the weather cooperates.https://goo.gl/LfvWnL
For Kyoto, again, it looks pretty full. Ginkakuji closes at 5 PM and Tofukuji opens at 9 AM. Unless you want to go to Fushimi Inari extremely early in the morning, it would likely be better to go to Tofukuji first. Fushimi Inari is open 24/7 and you'll be in Japan during the longest daylight days of the year. There are far fewer people to swim through in the evening as well. You're right that Maruyama Park and the Philosopherfs Path can be skipped during that time of year. Yasaka Shrine too - though you can walk through it in 5-10 minutes and be done with it. You could though see Chionin or Shorenin - both are much more satisfying. And between Nanzenji (don't miss the Abbot's garden) and Heian Shrine is the beautiful and virtually unknown Murin-an - see it before the huge crowds discover it and ruin the experience forever.https://youtu.be/OF1E7gGfv5U
Not sure what you are looking for in the next day in Kyoto - lots of shopping streets. The Kyoto Gosho is rather dull - better to see the Sento Palace or Shugakuin Villa, even though you need advance reservations and it's a 60 minute tour.
You might consider adding Nijo Castle instead of yet another shopping street you have.https://goo.gl/knQtMg
For Arashiyama, the Iwatayama Monkey Park is the same place you list twice. Be ready to sweat the 20 minute muggy hike to get there. And skipping the Otagi Nenbutsuji temple is a tragedy. The Bamboo Grove you'll be finished with in 10 minutes. The Tenryuji Temple next to it (especially the garden) is very renowned though.https://goo.gl/Neiowd
For Tokyo, Shinjuku Gyoen is not bad (the Japanese garden is very good, the French garden is not bad though you will again be too late for the roses, and the English "garden" is a joke), but there are better candidates - Koishikawa Korakuen, Rikugien, and some others.https://goo.gl/tAECfM
For Harajuku and Yoyogi Park, Sunday afternoon is best, if you can. For Meiji Shrine, don't miss the Meiji Gyoen Garden in the middle of it - most do, and just blow past it - so it doesn't get too crowded. You might be able to enjoy the beautiful irises in bloom then. The Hachiko statue will take you less than 2 minutes, aside from the line up of people trying to take pictures there. If you want to see a more heartwarming statue, go see the Hachiko Statue at the University of Tokyo.https://bit.ly/2W4KHHr
For Tsukiji, you are wasting your time. The fish market is now at Toyosu.https://www.japan-guide.com/e/e3013_market.html
You could certainly add more to Day 10.
For Day 12, why not take a day trip? Nikko, the Mt Fuji area, Kamakura/Enoshima, Yokohama, etc.
Days 13-4 look pretty empty. Besides the Ghibli museum (I hope you got your tickets), you could keep going 4 stations to Kokubunji and see the really nice Tonogayato Garden, or further along is the Showa Kinen Park - someplace you will never forget.