The old terminals had about 31 gates, with one of them used for Eagle (downstairs). Here's a map of the former Terminals 8 and 9 (there were two gates at some of the T-9 gates, IIRC):
http://www.geocities.com/citrus_air/jfk_termloc99.gif
The new design was to have 55 total gates, 38 of them for mainline jets and 17 covered jetbridge gates for RJs.
Here's a description of the original design:
http://www.dmjmharris.com/MarketsAndServices/39/99/index.jsp
Now it's only gonna have 36 gates, 27 of them for mainline jets, and 9 for RJs. Square footage sliced from 2.2 million feet to only 1.5 million feet. Instead of 200 checkin positions, only 67 or so. Instead of eight clubs (probably for all the OneWorld members), probably only 3 or 4. Total cost is down from $1.3 to $1.4 billion (varies depending on the source) to only $1.1 billion. Here's a description of the revised JFK Terminal 8 project:
http://www.queenschamber.org/queenschamber...an_airlines.pdf
The new terminal will indeed have fewer mainline jet gates than the original. Maybe it will be laid out more efficiently - or maybe AA will unload airplanes and then quickly move them to a hardstand to accomodate another arrival.
I liked the old terminal 9 (and some of the features of 8). But nothing stays the same for long. I liked 707s and AA's 747s, and AA doesn't fly them anymore.
Given that AA's JFK terminal rent is only increasing by a modest amount, the new terminal is not what's keeping AA from restoring $1.6 billion in annual pay concessions to the represented workers. Those were (and still are) painful, but they have nothing to do with AA's 1999 decision to replace the JFK terminals.