Good question.. I think that they are not directly comparable. To me, FSH is the most special Hermes store in the world... FSH certainly has more stock and more neutral color bags (my experience) and in Ginza you can be much more lucky and adventurous with the color. Having said that I got offered birkins/Kellys in both locations.
Agree with you colourbag that FSH is the most special H store in the world. I was lucky to be shown around the store and found out that many of the fixtures like the banisters and floor tiles are century old originals! Plus the bag showcases.... dizzying delights! Slightly off topic, but Serves is beautiful as well (to me the most beautiful store in the world), the sparkling mosaic floor tiles are actually the floor tiles from the original swimming pool which the store now sits on! Ginza is an architectural beauty as well, it looks like a giant tray of ice cubes!
Now, between FSH and Ginza, in terms of the general atmosphere, FSH is very old world European, and Ginza is very modern. Both are v wonderful and authentic H experiences.
For stock levels, B/Ks I believe are very very much available in FSH, in neutrals, seasonal colors and exotics. I think the key for walk-ins is that you probably need to click with the SAs, and I think it would be v v useful to have the SAs invite u back the next day if you weren't able to get one on the same day. From personal experience, I don't think time of day really matters. I have seen B/Ks offered in the mornings, afternoons and even right before closing.
I believe Ginza does set aside "daily B/K stocks" (ie B/Ks that are not spoken for by regulars or need to be approved by SM) and there is a good chance of scoring one if u are not particular with the size and colour. U really need to be there at the right time. The Ginza SAs don't really play games, but I think that they are on a watchout for reseller type clients before they offer you a b/k. And yes, there are alot more seasonal colours being offered at Ginza, and B25s and K28s are frequent sightings!
In terms of service levels, I think both FSH and Ginza have lovely and passionate-about-H SAs. I was lucky to have met with warm hearted SAs at both locations (and yes, I have received chilly receptions elsewhere before as well). I think maybe a simple Bonjour/ Konnichiwa works wonders as an ice breaker!
Prices in FSH are lower than Ginza. K28 in 2013 was Euro5650 (clemence, retourne) before detax and JPY871,000 (barenia, retourne) before tax.
HTH!! Good luck with the hunt!!