When will you be traveling? Sometimes a temple/shrine may fall off the radar during one time of the year but becomes a "must visit" during other times (ex: when flowers are blooming).
In general, I think the World Heritage Sites are also worthwhile (perhaps with the exception of Nishi Honganji Temple).
In terms of temples, some of my favorites are (the 1st 4 are probably better for a 1st time visitor, although Shisendo and Sanzen-in do not disappoint either. They're just less typical. The others I like but don't necessarily recommend unless you have certain interests):
* Daigoji Temple
* Toji Temple
* Kinkakuji Temple
-little Gioji Temple
Some of my favorite Kyoto shrines:
-Fushimi Inari Shrine