Adam Klivans notes that FOCS attendance is down, to about 172 registered attendees (which is like the reverse of announced attendance at sports events; more people show up than the official registered list), in comparison to STOC 2004, which had 100 more people.
The number of papers accepted at STOC this year was 72, in comparison to 62 at FOCS. In general though, (and I only went back a few years because I got tired of opening proceedings), STOC appears to accept 15-20 papers more than FOCS on average (75-80 vs 60-65). There was no significant submission increase (surprising given the trend lines for other conferences), and so one can only surmise that location had at least something to do with the low attendance. After all, if you are submitting (and getting accepted) more papers than before, and if funding is down, you'd have to be pretty careful about choosing meetings to go to, especially if you are not presenting, and are thus not constrained to attend.
Although the number of accepted papers is not out of the norm for FOCS, one does have to wonder whether there are really only that few papers worth accepting ? I suspect this is constrained by the whole multi-track vs single-track, conference-as-prestige-stamp vs conference-as-meeting-place issue, and FOCS represents one extreme point.