You have a long, long list of places you've seen, so I can only throw out a few ideas that you may have covered already. But there is always something more to see.
On the east side, if you haven't seen it, there is the Kyoto Great Buddha at Ryozen Kannon (
YES, Kyoto has a Great Buddha too). There are also some very good gardens at some of the subtemples of Nanzenji (like Tenjuan), and near the Philosopher's Path at the foot of the mountains you'll often see some lesser known temples like the Tanukidani-fudō-in which most people never notice. Near the Shugakuin Villa there are some as well, like Manshuin or Sekizanzenin, so you might explore those.
Another idea is go see the temples around Otsu in Shiga.
Not to mention there is more around Uji and Nara if you like. For the Nara Park gardens, there is Isuien and Yoshikien. The former is better but closed around New Year's so check your dates. With a foreign passport on tourism, you can go see Yoshikien for free.
https://goo.gl/LfvWnLSouthern Nara Prefecture has a number of places as well, and while a pain to get to, going to see the Akame 48 Falls just over the border in Mie is also something worthwhile.
There are some gorgeous places like Yatadera in Yamatokoriyama, or the Fumin no Mori in Higashiosaka for the hydrangea, but your timing is off. That said, along the Nara-Osaka border there are many good places with mountain views that you can access by ropeways.
If you haven't seen all the sights around Sanzenin, there are some places there. The Lake Biwa area has some places too. Most people concentrate on the eastern side, or go to Chikubu etc, but the western side is often ignored, with some great views for example up the Biwako Valley ropeway.
Can't remember if you've seen Minoo Park yet, but nearby there is also Katsuoji and Ryuanji.
That's about all the brainstorming I can do right now.