It's a shame that they aren't more popular; I didn't really see prefectural flags flown that much outside of government buildings when I lived in Japan.
My favorites are probably the flags of Niigata and Okayama. They have really appealing colors imo, and the symbols are great as well (especially Niiagata's).
Far right column, fourth one down from the top. I like that it’s a visual pun on the Japanese flag; the little red dot on a white field inside the larger dot effectively depicts a little Japan inside the larger nation, a microcosm of the nation itself.
It’s a very effective vexillological distinction of a part within a whole, while still maintaining the effect of the original flag design.
I also find it funny that it seems to be a flex on all the other prefectures, this flag subtextually implies, “We’re the most Japanese prefecture that has ever been, we are the essential core of this nation and our absence would leave a blank empty void. Don’t fuck with us.”