The biggest diferrence is the 36VAC output. Vectors and Centipedes have it, all the others don't. There might also be some minor differences in ancilliary voltages used for things like coin door light, etc. Your best bet is to follow the table at EF.
An interesting side note, all revisions of the AR-II (along with the AR-I) are all pin-compatible, meaning that you can safely interchange AR-II's of different revs without killing them. They might not work if they don't support the necessary voltages, but they won't die either. Here's the predecence list, where those at the top can successfully replace those below:
AR-II rev 3
AR-II rev 2
AR-II rev 4 (or AR-II rev 6)
AR-II rev 1 or AR-I rev 1* or AR-I rev 3
Note that an AR-II rev 6 cannot replace anything. Also, the AR-I rev 1 has an audio disable that some games might use, and is apparently missing from all other revs and versions.
For example, an AR-II rev 3 can replace an AR-I rev 3 or AR-II rev 6, etc. An AR-II rev 4 can replace an AR-II rev 1 or AR-I rev 1, etc, etc.