Online/split-screen co-op would be amazing. One of the fun things to do was using the grappling hook to take out cars chasing you, but there were only a few opportunities to do this in the game. Also make the grappling hook like the one from the bolo patch (multiple hooks, won't snap, etc). At least make it some sort of unlockable. GTA style cheats would be nice too. Change your wanted level, weather, flying cars, aggressive drivers, etc. Some more extreme weather could be interesting. Tornadoes, hurricanes, tidal waves....actually, random events in general. Also some sort of city/place full of destructible objects that respawn. Also trains.
Something equivalent to the sandbox program that comes Crysis. Being able to spawn a bunch of stuff and then get in game immediately would be pretty awesome.
Oh, and what andrespetmonkey said. More sand! Tons of fun driving around in the desert areas, but the forested areas pretty much had you confined to the roads.
@Disolitude
Kind of weird to say Just Cause needs to change in many ways considering one of the reasons for Armageddon bombing was the huge departure from Guerilla.
