I think it depends on whether or not you plan to visit Japan again. Tokyo and it’s surrounding areas are so diverse, you’ll have no problem filling the 10 days you have. While I enjoy riding trains, I don’t necessarily enjoy spending time on them when I could be doing something else. That being said, I do love watching the Japanese country side passing by, but I digress.
The first time I took my wife to Japan, we landed in Fukuoka, went as far south as Kagoshima and as far north as Tokyo. A LOT of train riding, but it was her (and her sisiters’) first trip and they weren’t sure whether they’d be back. I’ve been to Japan many times, so it didn’t matter much to me, but if I had my way, I’d prefer to take several trips, each to specific regions. I think it would be sad to miss out on places like Kyoto, Osaka, Hiroshima and Utsukushima (Miyajima) island, to name a few. Also Hokkaido is another part of Japan that I think is a must visit place. Hakodate, Sapporo, Otaru, Asahiyama all hold a special place in my heart and I love the climate. Hakodate is just 4 hrs by Shinkansen and the sakura (cherry blossoms) blooming at Goryokaku is a sight to behold.
If you want to visit Osaka in the future, you could perhaps fly into Kansai, then visit Osaka and Kyoto. It’s a 2 hr train ride to Hiroshima and Himeji castle is along the way.
So it really depends on what you enjoy. A lot to do and see either way. Hope it’s not your only visit and hope you have a great trip!