Best places to go in Japan?

First:

www.japan-guide.com/e/e2277.html

There is rainy season. While it is definitely not going to rain all the way through, it is not pleasant, and if you want to draw...you probably want to avoid those days.

Also I see that you are from Germany. Summer in Japan is pretty muggy and disgusting. There are a couple of spots that's pleasant enough, but those spots are not super great with architectures per se. I don't quite recommend it, but it is cheaper during that period.

From the choice you have, my first instinct is to go look at this charts:

www.japan-guide.com/e/e2014_when.html

This is the autumn leaves period in Japan and it is probably the second best time to travel (Best, probably, is cherry blossom season in Spring). Nice weather and beautiful fall foliage.

Also, if you are interested in festival time, this is one of the big festival in Japan:

www.japan-guide.com/e/e2286.html

The actual date differs depending on the locale as mentioned in the article, and moving about in Japan is quite difficult as everyone is traveling, but the bonfires and lanterns are quite pretty. Unfortunately, it tends to be pretty hot period.

As for the location...I say Kyoto and Nara probably is going to be your two best spots. They are both super-great places to visit as a tourist. Especially Kyoto, you will probably not run out of the beautiful temples/shrines/castle/etcs to visit in 3 weeks if you visit one-a-day, stand around and paint and so on.

Very expensive, and not really avoidable, however.

I doubt Tokyo is what you are after, but it is a super-big city and there are spots you can work with. Also, there are places nearby, day-trip distance, where you can find what you are looking for (Nikko, for example, is about 140km away from Tokyo and sounds like you'll enjoy it there).

Bonus with Tokyo is also it's central and convenient, if you want to hit different places from there.