Software requirements are different.
For example, with CAT OS, WS-X6516A-GBIC requires 7.5(1) while WS-X6516-GBIC is supported from 6.1(1d). Some customers prefer running general deployment( 6.4(8) is GD.) Both boards will be sold by Cisco.
With Native IOS, WS-X6516A-GBIC requires 12.1(19)E1 while WS-X6516-GBIC is supported from 12.1(5c)EX.