First time to Japan need advice on itinerary and ryokan
 

Hi everyone! I am planning to visit Japan with family of 4 in July 11~31. We are mostly into sightseeing while my sister (13) is into anime + manga of the sorts. A rough draft of my itinerary looks something like this~
Tokyo 6~8 days w/ day trips to hakone(Onsen?)/nikko
Kyoto 4~6 days
Osaka 3~5 days
Osaka -> Tokyo day before flight
w/ day trips hiroshima+miyajima and himeji + kobe for the beef (probably home base in osaka)
Might cut Kyoto shorter depending on our pace and head over to Osaka and might make a stop at either matsumoto,takayama,or kanazawa if the trip ends up going quicker than expected

Also we WANT to experience a night or two at a ryokan +onsen but i'm conflicted about where to go because the rest of the family is bringing suitcases and i'm packing light(backpacking is fun!) and Hakone was originally a day trip destination so i'm not sure if we should go to Hakone or try to find a place that is more convenient with a JR pass.
so where are the best places for a ryokan + hotspring combo in Japan?

Any must avoid attractions or must visit attractions are appreciated!

I trust you realize that this plan is VERY heavy on modern Japan and VERY light on traditional Japan.

IMO, Hiroshima & Miyajima don’t make for a good day trip. Consider staying overnight on Miyajima.

Either Takayama or Kanazawa would only make good sense if you have 3 nights for one or 5 nights for the pair.

Japan has an excellent luggage-forwarding option so you only need to take an overnight bag with you. Luggage-forwarding is called takuhaibin; here's the info:
http://www.japan-guide.com/e/e2278.html

If you haven’t already seen it, I’d encourage you to spend LOTS of time working with japan-guide.com

Good luck!

Consider Miyajima and Iwakuni in a day, but stay @ Hiroshima
https://knycxjourneying.com/2015/02/...-day-in-sanyo/

To me, Kyoto sights are more impressive than Osaka. But well, it depends on what your objective and what you want to see.
https://knycxjourneying.com/2016/11/...-little-kyoto/

That's fine as a rough draft. I think it is in the pins-in-a-map stage, where destinations have been identified but the details at each have not been worked out. For example, you have 3-5 days for Osaka. I could see the three days: one day Osaka (Universal Studios or whatever) plus the two day trips. But 5 days?

You have enough time in your visit that you sh/could spend two or three nights in Hiroshima/Miyajima.

Hakone would be a good option for an onsen ryokan. You would use takkyubin (first link that kja gave) for the suitcases.

Kinosaki Onsen would be a good choice for onsen and ryokan experience. It is 2 hours from Kyoto and about 2.5 hrs from Osaka.

Arima Onsen is another option. I haven't been there yet. It is closer to Osaka and Kobe. Could be a day trip on the "onsen bus" from Osaka station.

Spa World in Osaka is a good place for a soak in an onsen.

You don't need to go to Kobe for Kobe beef. You can get it in Osaka or Kyoto. It is expensive. There are other wagyu beef "brands", like Hiroshima beef or Hida beef in Takayama, and the "generic" wagyu (Japanese) beef that you might enjoy just as much.

Miyajima would be a good choice for a ryokan stay, even though it might not have the onsen options like the other places mentioned.

Re 'must see attractions,' here are two suggestions for your anime/manga loving sister: Ghibli Museum (http://www.ghibli-museum.jp/en/) and Nakano Broadway. Ghibli requires advance booking and sells out fast so as soon as you've got Tokyo dates, get tickets on line. And rather than going from Mitaka Station, go from Kichijoji. The Museum is a short walk through Inokashira Park and Kichijoji itself (one of the most popular neighbourhoods in Tokyo)ou is a fantastic area to explore. If you have time, you could also take Odakyu bus no. 6 from the Museum to Jindaji - maybe 10-15 minutes further on. This is a temple complex in a very green hillside setting full of walks, soba restaurants and adjacent to a large botanical garden.

Nakano Broadway is a short walk from the Nakano station via an oldfashioned covered 'shotengai' - shopping arcade. The area is full of small eating places. This, rather than Akhihabara (large, souless, confusing) is the place to go for anime/manga/idol figures and cult toys.

Sorry, should have specified both my suggestions are for Tokyo.