There seems to be a weird trend where the "good" options mean you get "better" results; less people die, or don't die, things just work out better, etc. It's not realistic. I'd love to see a narrative game where the morally "right" choices end up having bad consequences. Like say you do a questline tracking down a vigilante, and you can either cap them in the head, or turn them over to the cops. If you do the latter, they break out later, and one of your crew is their next target, and they catch them before you hear about their escape. You get to live knowing that your choice allowed for that to happen.
Obviously, not EVERY choice, or the game's just aping Dark Helmet's "evil will always triumph because good is dumb". But enough that you really question your choices. The "right" choice needs to NOT be the convenient/personally beneficial one. It has to be the one with negative consequences that you accept because you're standing on principle rather than coldly making decisions based on efficacy.
In ME3, the "good" choices generally got you the strongest army. I'd switch that. The Renegade choices should get you the strongest army, and make the finale the easiest. The Paragon choices should leave you struggling, but those who stick by you are fully on your side and highly motivated by your inspiring presence.
That ME:A is more complex than paragon/renegade is a good step, but I really hope there's choices like this, where the "good" choices are the ones that aren't optimal. Where you take the harder path because it's RIGHT, not because you get better rewards for doing so (which means you're just being utilitarian, not noble).