The last time I was in Isetan Shinjuku was in April, and they actually had a fair amount of high-end handbags there (I was particularly interested in Chanel and Balenciaga, and they had both - the boutiques on the 2nd/3rd floors are nice, from what I remember). In terms of other shopping areas, I would also recommend Roppongi Hills (my dad lives really close to there) as well as Omotesando Hills - when I used to live in Tokyo, I used to LOVE Omotesando (it was pretty close to my work). The Omotesando Hills complex (kind of across the street from the huge LV store there) has a ton of high-end brand name stores - I think they have a YSL there. It was really crowded when I went. My cousins (who are not from Tokyo) quiz me everytime I go; apparently these places are like tourist spots for non-Tokyoites to go visit too! Roppongi Hills opened about 3 years ago and Omotesando Hills opened this past year.. so these are very new places.
In Kyoto, I would definitely check out Gion - it's the old theater district, and it's great at night. I love Kinkakuji and Ginkakuji (gold and silver temples) - I also love the "love fortunes" at Kiyomizudera (another temple). One place that's great is Nijyoujo (the old Palace) - you have to check out their "nightengale floors"! They do have a huge department store attached to the train station (the main train station) and I remember there being some pretty good shopping there too (but Tokyo is still better.. I think I'm biased :shame: ). PM me if you have questions! I miss Japan sometimes