I have a JDM short gear 5spd in my car now. It's great because I feel it's the perfect balance for the mixed driving that I do (Street/Hwy, Canyons, Track). I'm supercharged which helps the balance and feel as well. I have not swapped to a 6spd for 2 reasons.. they are incredibly expensive and the 5spd is stronger for a boosted car. If I was NA a good setup is the stock 6spd, but OS Giken does not make a LSD in the stock final drive ratio anyone IIRC, nor are there any decent clutches that work with the 6spd input shaft. So therefore, the JDM 5spd, + Supercharger, + OS Giken clutch, + OS Giken LSD is my perfect setup. It's best of all worlds in my opinion and it took me 10yrs to figure this out.
I also have a JDM Type R, which is the short gears + 4.23 final drive. In an NA car it's a lot of fun in street, tight canyons, and tight tracks. It's a bit annoying on the fwy above 65mph. So depends how much hwy driving you do. The acceleration in 2nd and 3rd gear is a lot of fun in VTEC but not worth the HWY compromise to me for the driving I do. I still have this transmission collecting dust in storage. Saving it for a rainy day so I do like it enough to keep it.
I have also driven a 4.44 6spd, which has similar gearing in 1-4 gears as the JDM 5spd. It's just not for me. It can be a lot of fun but it's too busy for me when shifting.
On a side note: On my S2000 the previous owner put in an aggressive 4.71 ratio. I absolutely hate it. It's fun when you want to feel like you're rushing thru the gears but next thing you know.. it's only 45mph and you're in 5th gear and you've hit the next stop light. The part I hate the most though is at 75mph i'm at nearly 5k rpms. I also hate that because the gearing is so short.. it's makes the car really jerky on/off throttle. That's by far the most annoying when you're trying to feather the throttle mid-turn.
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btw.. I have a theory on why the Japanese like short gearing, especially short final drives. I suspect that because they tend to drive slower speeds there and the streets are generally tighter as well as tighter tracks it might suite their driving styles better. It's just a guess on my part. I have yet to rent a car and drive performance car there.
Even one of the shortest/tightest tracks here in SoCal (Streets of Willow), the stock JDM Short gears suites the layout the best. The gearing also works for Buttonwillow and Laguna Seca. Seemed fine for me at Sonoma as well. The video in my signature has some mention of gearing and it's differences.
. Staying in boost or tracking it has a much bigger impact. 
