I currently do not know what is currently planned base wise as this version does not contain all the contents (Especially the base just not being there), but id like to throw in those ideas, in case some of those weren't thought of:

Base:
Extra hostages roster: The base could hold the extra people you save on your missions, allowing you to switch your team when out of a mission sector;
Functional base: The option to be able to go roam in your own base and use workshops and talk to your team members (Creation of the Squad leader character, since all the recruits answers to him/her), workshops being crafting/tweaking/upgrading gear/consumables;
Customizable base: Allow you to define the rooms and what they contain;
Interactive base: Merchants coming to offer trades, raiders attacks, hazard events (Gas leak, explosions and so on, causing the base needing repair) (Think like XCOM bases when aliens invades them)

Mission environment:
Lootable crafting materials (Lockers, crates, anything that looks mundane in the environment, materials can vary a lot but for the sake of simplicity for the development of the game, can be summarized in main components, like wood, metal, stone, radioactive, energy, medical, and so on) All given automatically after a successful mission, if emergency evac is called, only give what is manually found;
Engineer class: I'd like to see a class in the future updates that allows you to build covers/turrets/mines on the spot, and with lootable crafting components, this is a viable thing.

Infinite playability:
I know that in the final release there will be a story and an ending, but i'd really like a never-ending mode for this game, especially if missions are limited as they are right now, i'd play the story once to see the campaign, then play a never-ending mode so i can keep progressing forever, or simply allow the game to continue after the ending.

Persistent characters:
Being able to export/import your favorite character through previous games, especially useful if coop multiplayer is ever planned.

Thanks for the feedback again :)

The base building idea you are pitching is very similar to our original idea. Unfortunately in game development a lot of ideas have to be cut in order to finish the game. If we do a sequel then crafting and base building will definitely be part of it but we don't have the luxury of taking the extra year to build and polish those systems for this game.

We're actually going for the infinitely playable version rather than having a linear story. There will be some "emergent" story and questlines but nothing set.

We should also have persistent characters. Since every character is a merc, you will have the option of recruiting surviving characters again in the next mission, but they will be more expensive. We'll have a blog post to cover this in more detail soon.

I do hope for you folks that it will turn to your advantage, this game has fun potential.