Just wanting to get my 2cents in (and please, be gentle, writing in english after being awake for almost 48 hours is kinda messing with my brain... )
From what I've read in the comments, there is truth in saying that most audience members won't really gel with an ambiguous and shades of grey kinda factions.
Both the EFSF and Zeon have some really complex themes going on. I do believe that in order for this to be something of an hit they should emulate what they tried with Warcraft, but I say make them separate movies. Now I can hear most of you grinding your teeth, but hear me out.
As some of you said, stick with the Star Wars formula. Make Amuro (assuming they are going with the original story for an adaptation) the hero, focus on him. Make people fall in love with the character. Make people fall in love with the EFSF and most importantly make them HATE Zeon. Show just how far Zeon is capable of going to achieve their goals of Independence. I say show them being relentless, Empire like. Show the destruction they are willing to create. Show the conflict but keep our heroes, heroes and villains, well.. villains. Make Char the Emperor of this movie. Make the best, most kickass action movie/mech movie/space opera possible.
Make people love the heroes, and love to hate the villains. I do think that this is the way to make this a success.
NOW put down them pitchforks and torches please...
IF, and this is a big IF, this is a sucess, twist the audiences expectations... make a sequel focused on Zeon. Show the other side of the Principality. Their plight, The reasons that make them want Independence, and MAKE THE EFSF the villains. Show that some of the good guys aren't all that pure, all that nice. Show Char as the charismatic leader that he is. Show Amuro like THE target to bring down. All of them Zaku pilots that he's killed. The families that he's ruined. Make us question the first movie. Make us wonder "Did... did I just root for the bad guys?"
And as usual, this is Hollywood that we're talking about here, make the third movie the big confrontation. Let us go into it on a grey area just like both our heroes and villains.
Sorry for the Wall of text but I just wanted to share what I was thinking.. I'll get myself out.