innocent villagers being murdered by goblins will be the primary wrong-to-be-righted for heroes
Only if 1) The heroes have nothing better to be doing (Say I was on a mission handed directly to me from my god that was about urgently preventing the end of the entire world. I'd have no reason to care to stop a few goblins when the people who are being murdered will die anyway if I don't finish my task)
2) We're going under the assumption that those villagers are innocent and those goblins are in fact evil.
3) There's no-one else currently acting on this.
The villain on the other hand would start with an entirely own motive that may have nothing to do with the scenario at hand.
So do the heroes?
Like, literally unless you directly write that the only reason for the heroes to exist in the setting is they want to deal with these goblins, then the heroes have other motives.
But if you're writing the heroes to be directly tied to these goblins... You can do the same exact thing for the villains. Have their motives tied directly to the goblins.
I'm not sure how you don't see the fact that you're forcibly writing heroes into things while at the same time giving villains tons of freedom and saying it's impossible to work around this arbitrary freedom you gave to the villains and never to the heroes.
Heroes and villains are equal in writing. There is no inherent bias that leads either side to be different. The fact that we're here on a forum for a game that shows exactly that, with the evil and good routes both being the exact same story beats with only minor differences shows that.
I haven't played Mass Effect, but if those Reapers are the meanies, the goblins in our scenario, making peace would only be a variant of a good playthrough. You probably have the same alliances through most of the campaign and then probably only anger one friendly party if you don't follow through with mass murdering Reapers. Somehow abusing the whole Reaper-situation to take charge of a part of the world or allying with the meanies because you hate the others more would be two different evil scenarios that would not work with the same story moulds.
In Mass Effect, no-one cares if you destroy the Reapers (Good ending) or enslave them (Bad ending).
Both situations involve the exact same story to get to this point. You continually fight against the reapers. Then a big ol' Deus Ex Machina weapon appears and you buy time while it gets built. Then at the very end you just pick one of 2 options, exterminate or enslave. With the only notable aspect is that you're locked out of the best version of either ending (The one where allies don't randomly die for no reason) unless you played 100% good or 100% evil up to this point.
As far as "Taking charge of part of the world" vs "Allying with the antagonists" that's not really a particularly scenario changing thing. Especially when such a thing is only relevant as the literal last action in the game (Much like the Netherbrain choice pre-Epilogue) all it surmounts to is having a different ending cutscene.
Which is the major thing with morality in games. Much of the actual differences only come from a simple ending choice, to determine a final cutscene. It's never about the collective actions you made (Or, when it is, such as in Fallout New Vegas, all it really surmounts to is still just an altered ending cutscene showing the aftermath of the various choices you made - Same thing happens in Witcher 3 too)
As such, it really doesn't require entirely different scenarios for different goals to be utilised.
Perhaps if you wanted to build up to the goals, they might differ... But not often in dramatic enough ways that can't be incorporated as options in a single scenario.
For example "Taking charge" and "Allying with antagonists" can still use the same build up of allying with the bad guys and furthering their goals for the most part. The key difference would be the choice to leave the leaders alone or to remove them and take charge. Which can co-exist alongside good routes to ally AGAINST the antagonists and shut down their goals and then you can still have your key choice about making peace with their leaders or removing them (Oh look, good and evil routes have the exact same end result of either taking out the leaders or letting them live! With only a minor difference in the actual path to get to them. Funny how similar things can be...)
