Best place for hikes/shrine visits?

I'm going to be spending a week in Japan in April for my vacation. I plan on making a solo trip to visit shrines and natural/historical places. I was thinking Kyoto is the best place for that. What do you guys think? Are there any other better places? This will be my first ever trip to Japan.

Thanks

Kyoto will be the most tourist-friendly among all historical cities of Japan.

What's best depends on what kind of historical stuff you are looking for....

http://www.japan-guide.com/e/e623.html

In my opinion? Yes, there are!
Kyoto is very crowded during cherry blossom season, so I'm not sure if you can fully enjoy all the sights.
You might also consider Nara Prefecture (e.g. Mt. Yoshino or the Asuka region) or Mt. Koya.

Shikoku is also extremely beautiful in spring, but not as crowded as Kyoto.

Kyoto is by far Japan's best destination for historical sights. But for nature and hiking, there are better destinations, although places like Kurama and Hieizan also offer a few nice hiking opportunities near central Kyoto:
http://www.japan-guide.com/e/e3933.html

I also like the suggestions of Yoshino and Koyasan.

April is still early in spring, and many of the higher mountains are still closed for hiking, e.g. the Japan Alps or Hakusan.

The Kiso Valley could be another destination:
http://www.japan-guide.com/e/e6075.html

Or the Kumano area:
http://www.japan-guide.com/e/e4950.html

Of course, Kyoto is the best!
But as the above mentioned, there is so crowded from late in March to early in May.
Altough all tourist sites are very crowded in the season...

I can recommend you stay Kansai-area (Kyoto, Nara or Osaka) and go some places?
There are good convenience of access and many historical/natural places.

In Nikko and Kamakura, there are historical shrines/temples and beautiful nature, if you stay a few days, I think Tokyo-area is worth considering?

And you can research Izumo and Ise grand shrines as the greatest shrines.
http://en.wikipedia.org/wiki/Izumo-taisha
http://en.wikipedia.org/wiki/Ise_Shrine