That's definitely quite a bit, but even $1500 would have the two of you covered and then some for a week.It would all depend on your preference for western versus Japanese/business hotels, and what your culinary preferences are. Obviously shinkansen tickets would be quite pricey, but I don't see you fitting in 2 large cities in a single week.
With delta I'm getting $3551.60 round trip for 2.
Interesting. I noticed the Wikitravel front page changed recently, but wasn't aware there was Internet drama since before those sites appeared to be mirrors.
Just note that the wikitravel community has moved over to wikivoyage.org following some internet drama