I have now finished Island Thunder:
The AGS-17 has been removed, most AGS-17 turrets were turned into machine gun turrets, however in "Ocean Forge", you still need to secure the AGS-17, it has a new model and is now an "packed up" AGS-17 that is not set-up to fire and is placed down on the ground. (So it's unusable.)
Every mission has a new ending CGI cutscene.
Some of the Specialists have changed weapons:
Harold Gordon uses a FN FAL instead of the M16A2, Klaus comes with a 9A-91 with 15 spare magazines instead of the MM-1 and Jack Stone's SR-25 is supressed.
The Distance Fog is greatly expanded in certain maps, in Hidden Spectre you can see the other end of the Airfield from one end for instance. (Making surviving the ambush easier)
Less Vehicles and less enemies attack the voting polls in Liberty Storm.