As advised I shifted things around and left Nikko as a day trip, seems reasonable, and frees up some more time on the latter part of the trip. Thanks for that!

For rail I just want something that will work for all my train legs, without the hassle of having to deal with machines or any other middlemen.

Rail legs are:
1. Tokyo - Nikko (RT)
2. Tokyo - Kyoto
3. Kyoto - Osaka

While on topic; recommend a good stop during the Tokyo - Kyoto leg for a clean view of Mt. Fuji?