In addition to what Jason mentioned in his posts, you should not try to achieve any kind of 3D modelling using sprites, unless you want to make things really hard and inefficient for yourself. Some challenges are worth not taking.
FYI, it's generally the other way round i.e. sprites are created out of 3D models.
For your particular requirement, it's better you go with polygonal mesh.
Instead of just a RTS at universe level (which is also quite unique btw), you can think up something in terms of virtual reality.
Which means, not only can you kill to win, you can bribe to win, or assasinate some opposition member(s) to slow down their charge.
That brings in endless possibilities which I can't even begin to summarise here.
In order to create individual stories to follow players, you can use some psychology sketch for each player before their hero gets designated to them. There are sites to do a psychoanalysis for people, like rembrandtsketch, etc. This way player can feel completely in sync with her/his character. Good, bad or ugly, this can bring out the true colours of a player.
All I am saying is, RTS has unfortunately become a saturated genre, with not many new stories comiing up.
Even the 4 points you mentioned seem to be a cover song with new musical instruments.
Since you can use dynamic content generation as well as a match can go on for as long as some human lives, then why not make it "real".
If you really want a twist then this can be an idea which isn't cliche and hasn't been tried before.
Your character (who is also the main yet expendable protagonist) kills all in the way, as per his orders and encounters in the end... himself.
Then the true fact dawns on him.
Basically, all the soldiers were given orders not by a human, but an alien humanoid, who disguised himself as a human, and created a race of clone soldiers, which were ofcourse expendable.
In the end all these soldiers were anyways going to die (killed, if you may).
The post apocalyptic era, is nothing but a final cleansing, tried by the invading humanoids that just needed Earth to create a colony of their own, and devised an ingenious plot of using human clones against humans themselves.
However, your protagonist realises that he himself was cloned out of none other than a human being who led the last colony of surviving humans.
With that you also have a scope of having a Part 2 for the game, with the underlying theme as revenge/revival ofcourse.