Trip to Japan: Needing destination suggestions

I am heading to Japan this Wednesday with my Sensei's last group of students since she retired last year. This will be my 4th trip. Usually, each trip I try to find a handful of places I haven't been to yet as well as revisit some of my favorite shopping havens ;) I was hoping to get some ideas from here.
I am not too familiar with the Kyoto area and I will be heading back there this time around. I have been to most of the popular tourist spots in the past, so I'm excited to check out some other places.
Here is a list of places I may visit, potentially visit, or revisit.
Kyoto
KyoAni shop- never been here yet and it's in Uji-shi.
Tozando sword shop - my friend is a huge samurai otaku and I wanted to check this place out
Osaka - this isn't too far from Kyoto so I was thinking of a day trip here of just walking around and possibly checking out the 3 Mandarake stores here.
Toyosato - K-On pilgrimage ;)
Miyajima
I really have no clue what is around here but we are staying on this island again. I may just go back to the mainland and just hop around on the trains.
Tokyo
Tsukiji fish market - never been here but my sensei is dragging me here this time
Akiba - duh ;)
Nakano - revisit
Ikebukuro - I always stayed around the south side of the Yamanote line and may venture to the northern parts of the line.
Goodsmile cafe - Madoka love!
Chichibu - possible HanaIro pilgrimage - not sure yet
Washinomiya - possible repilgrimage depending on time
Shinjuku - for the Squenix shop and the AnoHana Secret Base at Parco
Volks store
I have a lot of places in mind for Tokyo, but Kyoto is still a bit lacking. Not really too familiar with the area.
If anyone can provide any ideas, I'd appreciate it :)
Dang seems like I have to upload a pic to post. So uploading a random pic from my first trip.











Definitely check out the Manga Museum in Kyoto. There is an awesome Mandrake store in Shibuya I visited last trip. I would also go to Yokohama as there are lots of fun things like the Ramen Museum to visit.
Hmm, thanks for the tip about the Manga Museum. Haven't been there yet. I have been to Shibuya's Mandarake. It's pretty cool place underground.
If you're going to Miyajima, you should visit Itsukushima Shrine, there is a famous giant torri gate there. You could also take the ropeway to Mount Misen or just stroll around and have fun with the wild deer. There's also Daisho-in Temple on the way to Mount Misen.
Make sure you try Kakiyaki (grilled oyster) and Hiroshima Okonomiyaki. It's yummy.
I've never been to the top yet. I wanted to conquer the trails lol and not cheat by using the ropeways. I think I will give it a serious go this time and actually try to walk up the mountain.
Yes I love the Hiroshima Okonomiyake! <3
In Kyoto the Golden pavilian is worth visiting, as is the old Imperial Palace. In Kyoto station ride the escalator/elevator to the top to get a free view of all of Kyoto.
Kinkakuji is definitely cool, have been there. I don't think I have been to the old Imperial Palace. And yea the Kyoto station is pretty cool.