About the game idea
This idea is very rough...The player takes control of one, or a group of four humans, I haven't decided yet.
The gameplay revolves around setting up basecamps,planning attacks, traps, emergency retreats and eliminating priority targets.
The player should plan his strategy in an overworld type of map.
I have two Ideas about the fight system:
1. Round based like jagged alliance. In this system, the user would take command over a group of Humans. This fight system seems very straight forward. I only have to think about a good "chance to hit" and a "can see/cannot see enemy" algorithm. Plus I like the choice you have to make to shoot for the head, body, legs, arms...
The bad side of it is that the whole gameplay is solely on strategy. It isn't that exciting I think.
2. real time fight system like "Alien Swarm".
I really like the simple but exciting gameplay of alien swarm. Here I would let the player control only one human. It also would have potential multiplayer fun.
But with this system i have the problem of bringing longer range combat into 2D space. In Jagged Alliance, you just move your view to the enemy, you have the time.
My apologies for not being able to carry on before. Take into account what Tom has told you. The forums here are very individuated in terms of the information provided. For example while I can provide advice (replace advice with: my overegotistical opinion ) I could not for the life of me tell you what programming language you should use to best service your needs.
With regard the lore aspects you could also separate that into a post and throw it into the Writing for Games Forum asking for feedback, ideas for improvement etc.
At this point you really need to define whether you are going to use a turnbased system or a real time system. You have already starting noting the strengths and weaknesses of both systems in terms of your fighting. But given that this will be such a core part of your basic gameplay, you need to make a decision. Once you have done that then you can establish a path upon which to build your game. Don't forget if you decide for example to choose a turnbased system, progress two months into it and say I chose wrong I really need to implement it as a real time system. You have the ability to backtrack. The lessons you learnt while going up a false path are still valid and moreover in future decisions like this you are more likely to recognise similar wrong paths in the future. It is not failure to go backwards and start again.
I like the idea you are playing with regards setting up basecamps (or forward fire camps) and emergency retreats and I think if you can incorporate this successfully into an ebb and flow of warfare design it could be quite powerful. What might be interesting is that, as you progress through each level you are literally building on the preceding level and when at a point the enemy counter-attacks in such a way as to push you back (possibly several levels) that the camps and retreats you have built are there for your support. Implementing some sort of resource system to limit how many camps etc you build could ensure that you don't overdo it at the same time delaying to build camps could also provide the enemy time to build their own troop (monster) levels up.
I would like to see more of your idea expressed though, to gain a better understanding of what it is you want and where you want to go with it. Try and avoid using other game's mechanic to describe your mechanics, because not everyone who reads these forums may have played the same games, rather describe your mechanics in your own words.
Hope this helps