We're currently thinking about the map and the general interaction of the game. I'll make a more detailed blog post in next weeks about it, but in practice my idea was to have missions. Check this quick mockup I made:
the red missions would be the one to advance the plot, while the blue one would be secondary missions, using base map but with randomized content (enemy, loot, etc).
The idea is that on Easy/Normal mode you can only play the red missions and go on fine, but since we know that SOME players absolutely like to grind, playing in Hard/Impossible difficulty means that they should also complete some of the blue missions to get more EXP/money/resources.
For the exploration gameplay, each missions has isometric maps to explore, so I really feel that there's no need to have even an exploration part at a biggest level (planetary exploration). Besides I'd like to think that after defending the whole planet they have already explored it, it's only some small areas that need to be explored at a more close-up range (a bit like the modern world warfare).
There will still be a map for your movement inside the colony, to choose which character to talk to, and so on (and yes they'll have an indicator if they have something new to tell you as requested!).