Had a fair bit to read here, but I got through it :p
I'll separate my thoughts on the aspects you asked for in two separate headings:
Story
What I like about this project is that while the story is not necessarily new and creative, the entire thing comes together so nicely that it doesn't have to be unique. The fact that you have a story that isn't so thick with cliche that you can smell it from 3 threads away shows you've put time into this. I also think that it's something that could actually happen in the setting provided (economic crisis and some powerhouses trying to get ahead in the world, which one could technically argue is happening in the world today).
Gameplay
Well, this is where most of my criticism is going to come into play. Some of it could potentially be part of Story, but I figured it would work in either heading.
Something I really like about this project is that you have set a goal, and I personally feel that you've achieved it. And that's replay value. By having three different factions, one can play through this game a number of times and not really have to worry about having the same game three different ways. At least, that is the impression I have gathered based on your first post (different goals lead to different destinations).
As said before, something you're going to have to put extra care into is balance. I have no experience with GuBiD's TBS so I don't know how it works, but I definitely agree that it will likely need to be tweaked in order to obtain that "RTS" feel you want to implement. You definitely have your work cut out for you with the number of different game scenarios and units.
Something I thought of while reading this (and I am not sure if you have thought about this as well) is the carry over of units, and how they will grow. You stated you wanted an RPG feel, so it leads to me the question: will units that have taken part in battles grow in strength or rank? For example, say you name your units, and have an Assault pilot named Frank, if he stays with you through a number of battles, will he become "Corporal Frank" and gain bonuses? Or are units solely upgraded through R&D?
Something else I thought of is, is there a set path to this game? Or is this non-linear. Do missions HAVE to be won, or are there certain situations where a defeat does not lead to "Game Over", as is the case in war. What comes to mind first is Star Fox 64, where you could lose some missions, and be put in a different path. Ultimately you go to the same ending, but you aren't forced to win every battle to get there (because let's face it, who can win EVERY battle in war?)
Now, you're like me, where we tend to bite off more than we can chew (I have a number of stories set in motion for potential games, some started, some not, and most are way too ambitious), but something you might consider is a "Scenario" aspect rather than the storyline, as you find in most RTS games. Basically allow the player to have a Quick Play option. Not sure how hard that would be to add in, as I've never done anything close to this project before, just another thought that came to mind.
Also, a question on how "Heroes" will work. Are they typical units? Or will they be special mechs, not limited to the class types you mentioned in the first post (as in, is Hero 1 a Ballistic, or is he a separate class, with his own unique strengths and abilities?)
And since I'm on the topic of classes, how do Lieutenants work? Like, are they the same gear simply with different abilities, or are they all different classes (which means they'd look different, and "Lieutenant" is just a name). Or, am I wrong on both of them, and they are simply upgrades to units you already own? Like, a Lieutenant UAV.
Anyway, I think you have a great project here. Had a lot to read, so it's only natural that there's a lot to say :p
Here's my first PCP critique for your project.
