In truth, there are not many "unpopular" areas of Kyoto. That is to say, no one is going to say "oh no, don't live there" if you don't have kids (that's when school districts, child safety, etc. come in to play.)
Today, Kyoto urban culture has largely divided into Kyoto Station area, Shijo area, Kitayama area, and Fushimi area. -Kyoto Station area is growing in development and popularity for food, entertainment, and shopping. -As a direct result, the Shijo area is struggling. It has fallen behind on pretty much every front. On the other hand, this situation combined with a spurt of apartment construction in the last 10 years means there are some great deals for the location. -The Kitayama area is very wealthy and highly popular but it became so expensive during the bubble that development stopped and it feels incomplete. But if you are into quiet and beautiful neighborhoods (Kamogawa River), Kitayama, Shimogamo, Shugakuin, and Matsugasaki are wonderful but again, newer buildings are very expensive... - The Fushimi area is growing in popularity with young/middle age (30's/40's) because it's inexpensive compared to most other wards, there are many shopping facilities, and lots of B-kyu food options. It's the new "in" neighborhood for young families.
I personally think Sakyo-ku (Kitayama area - Kitayama, Matsugasaki, Ichijoji, Shugakuin, Shimogamo) is one of the best places to live in all of Japan but perhaps I am biased. That said, it can be boring after living in Tokyo but it's really a never-ending case of "grass is greener on the other side".
If I to recommend one particular neighborhood in all of Kyoto it would be Demachiyanagi. It's really a best of ALL worlds location. Access, culture, entertainment, nature all achieve the best balance in Demachiyanagi. The one drawback would be that most buildings are old so newer apartment buildings definitely are noticeably more expensive.
With Kyoto, you don't have to get too fixated on "where". If you are physically able, Kyoto is one of the most bicycle friendly cities in the world. City geography and parking facilities both support the bicycle lifestyle. I have put many more miles (probably 4 times as much) on my mountain bike than on my car.
So no matter where you live in Kyoto you can go anywhere by bike.
With 90k/month, you will be able to find a decent sized apartment in a neighborhood you like.
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