Turn-based combat

Yep, but there is no game in the background. All areas are up for being combat areas. You can have one pirate party on your ship, and your own squad on their ship. You can have a third faction on your second ship, and this same faction exploring a derelict with another squad

The support for multiple battles across multiple spaceships is there, and has to work to some degree. Add in ship-to-ship combat and it's a very complex matter. Turn-based would work here, but it would be extremely long-winded battles in these larger scale situations. We also have to think about player awareness, the fact that the player can only concentrate comfortably on one area at a time. One of the big problems with a game like this, where everything is packed into one scene, is managing game play in a way where we try to minimize the need for the player to pan around the map frantically to keep tabs on multiple areas.

The problem mentioned above will be there, to some degree, but we can try to minimize it as best we can. However, there is no way to pause the game in the background, because there is no background game. It's all in the same scene and everything is accessible While turn-based would solve player awareness issues due to being able to show one move at a time, it would bring a plethora of other issues. And the more crew members the player has, the more the turn-based problem compounds. In the end, when the player has over a certain amount of crew members he would most likely wish the battles to be real-time so he can quickly get over it in many situations.

By going even deeper, we need to think about what the game is aiming to be, because this experience we're having with Space Haven is really teaching us that you cannot have all games packed into one game. By having a base-building, more large scale unit simulation game your inevitably going to close of "turn-based individual unit movement" type of game style. The balance between trying to implement as many cool features as possible and still having enjoyable game play is tricky, it's not something that can be done without careful judgement.

The original X-COM games were great because their focus was on turn-based combat, and a more simplistic base-building game. Furthermore, these two modes were completely separated, giving the player a comfortable amount of needed awareness for each mode. When in combat scenarios, all the player needs to do is focus on the next turn-based move. When in base-building mode, all they need to do is concentrate on what to research and what to build next. There is no overlap, of having to manage multiple areas at the same time. The problem with Space Haven starts to arise when the player needs to keep tabs on multiple areas at once, both own fleet and the enemy fleet. All we can do is try to minimize it as much as possible and create scenarios where this is taken into account.

The combat might still evolve, if we can find some great things to add or come up with some ideas that would enhance it from what it currently is! We do know it is simplistic.
And on an ending note. It's not impossible that there's going to be a spin-off or another game made with the same base as Space Haven, but focus turned more on turn-based combat and other game play elements supporting just that