I'm playing through the game right now and reached the mainland, and overall impressed with the game so far. I appreciate that many map sectors have something interesting going on, and exploration nets resources that continue to feed the loop of hiring mercs, liberating territory, resupply and hiring more mercs. I find I really need to 'live off the land'.
I also think the devs did an OK job with the strategy layer, with sector inventory ('sector stash') streamlined as things like crafting is now tied to the weapon itself, making each one feel more customized and valuable.
The omissions are, as many mentioned already, the absence of online shopfront for gun purchases, no real market for guns, and crafting resources scarcity seems contrived (i.e. gunpowder). I do miss vehicles so far and especially Skyrider, but that puts into perspective of how to think ahead and coordinate mercs' actions against time.
Sometimes the dev's desire to weave a bit of narrative or drama into certain events goes against my expectations for a Jagged Alliance game. One such example is the Haunted Mansion sector where the second phase of the event is some special kind of scripted bullshit that puts everything into a lurch. Sure, it tests the mettle of your squad as they react against stacked odds and that act in of itself tests one's resourcefulness and skill, but I never experienced anything like that aside from maybe Drassen counterattack in JA2.