My idea is this, take the customisation of the main character to the next level. Let us choose which race we belong to. Be it Human, Quarian, Kroga, Salarian, etc, let us pick to be either a male or female from that race.
"You're crazy, Vespervin" is what your probably thinking. "Why would a Krogan work for the Alliance and/or the Citadel?" Think of this. Make the back story for the character somewhat generic. Make it so our character is from the Terminus Systems and has no allegiance to anybody, some Mercenary or Freelance individual with a particular skill-set that the Alliance/Citadel needs. Eventually, our character could be drawn to the cause, or do the job for the credits and glory. This way, we could be any race and it would still make sense.
Your idea and mine are compatible. I was thinking of allowing the player to pick which race they belong to. Given where they're going with DA:I, I would think it's a safe bet that the level of customization will make it in the next ME game.
As far as the terminus systems go, I was thinking that the protagonist could be some hired hand. A contractor. You work for a company that provides transport and security to companies that send their scientists, engineers, etc. out to far reaches of the galaxy to mine, conduct research, explore for resources, yada yada yada. All in the name of "technological advancement". Maybe the goal is to take space travel to other galaxies. Since the company who hired you isn't too big on following strict codes of ethics and thrives in ethically gray areas, they are headquartered in the Terminus Systems; outside of the Citadel Council or Alliance jurisdiction.
Your background as the ships captain can vary. Yes, a captain! That way, it allows us to have a "Normandy" of our own. Maybe we can outfit it with cool upgrades...I digress. Much like you alluded to, your character is escaping something. My thought was that you are:
1) Human - disgraced Alliance soldier; court marshalled. Your actions were necessary at the time, but violated military code. It was either you and your squad dies or you commit this war crime.
2) Turian - disgraced C-Sec officer. Your partner died under suspicious circumstances.
3) Krogan - disgraced clan member; exile or death for something you're accused of doing
4) Quarian - took the pilgrimage and never looked back.
5) Asari - Former Asari Commando; you're blamed for the death of the Matriarch you were protecting...falsely?
6) Batarian - You pissed off some slavers that you worked for.
The story evolves as you learn more about the people you're working for. A few members of the team, who become your companions, have some misgivings about what's going on with the research and implore you for assistance in looking into it and getting off of the planet to inform either the council or the alliance. While the council or alliance lack jurisdiction, the real plans of the company are a threat. Maybe not a threat in the sense that the galaxy will be destroyed, that hand has been played. It turns out, the company is just Cerberus in new clothes and they intend to overthrow the Citadel Council and install a new order that is, of course, human centric.
Given that your companions are from various races, this revelation can create some nice relationship dynamics. If you're human, the non-humans will question your motives and wonder if you are too pro-human. If you're non-human, this can create some tension between you and any humans in your group.
Just something to keep my mind busy while I wait for the next game...