While I think that the Rogue Trader game system could work, wouldn't it be easier to, oh I don't know, keep the character generation method that that game has? Start everyone with the 2d10+25, in their stats, but rather than selecting the planet, they come from they choose their race. That way you don't have such a large list of different rolls for different races, and you can include some racial benefits as well, such as Krogan/Vorcha regeneration, or Asari natural biotics, etc.
I agree that keeping the 'core' races, Human, Asari, Turian, Salarian and Krogan would be the best idea, and add the others later.
Also, the Hanar are apparently strong, but outside of water, not very agile/fast.
I'd also use both ME1 and ME2's ammo system. If you roll the 96-100 your gun overheats, and you either let it cool down slowly - meaning you can't fire for 2 rounds or whatever or you replace the heatsink. This keeps the feel of both games.
But all in all, I think that the Rogue Trader/Dark Heresy system would be a good match for mass effect.