Which games similar to Mass Effect?

I always got a pop-up every so often via PipBoy communication that a Settlement was under attack and that I had to go there to defend it.
But in my case, I'd prepared so well all I had to do was watch the show as my Settlement defense turrets obliterated whatever unfortunate Raider group was arriving.

But I gave up doing the main quests anyway once it became apparent I had no control in the direction I was taking the plotline.
These were my goals:
1. Take out Elder Maxton because he was making the Brotherhood too xenophobic so I could change their policies. Some of that was actually planned, before it was removed from the game. See here for the proof:

2. Take control of Liberty Prime and give him to the Minutemen. Because I trust them with him more then I do the Brotherhood. Also, I would have the control authorization, so I'd say what LP does and to whom.
3. Conquer the Institute, not destroy it. I wanted to make the building into my own personal science settlement and replace the untrustworthy personnel with scientists sourced from the wasteland. Also, some of the Institute personnel weren't 100% approving of the direction they were taking, so maybe I'd have gotten to keep some of them around.
4. Make peace between the Brotherhood and the Railroad. The Minutemen will accept any faction as allies except the Institute, so they would follow your lead as long as you were still loyal to them.

As regards NukaWorld, I wanted the option to turn that into Minuteman controlled Settlements, because I have no interest in aiding Raiders.
But I can't play that expansion until the mod I am working on for it is complete, because I think it's best that I test the mod in live action gameplay, for bugtesting purposes.
But as I am not a good Fallout modder, I am uncertain if I can ever finish this task and by extension, be able to play the DLC.
Well, at least it gives me something to look forward too, knowing I still have some story left to play.
If I get past the current mod problem, I will see if I can mod the ending of NukaWorld to make it possible to claim the Settlements for the player Aligned faction, whatever it might be.

I think there is a way to turn the Raider gangs against each other though, if you don't allocate them terrority to control inside NukaWorld, they turn against you, most likely as part of Open Season.
The mission flow was set up so at least one gang gets eliminated.
I chose the Disciples because they are the most antagonistic of the Raider Factions.

For me the two raider groups that stayed loyal to me were the Disciples and the Operators, with The Pack being the ones who turned traitor. The Operators got Galactic Zone, Dry Rock Gulch, and Safari Adventure while the Disciples got Kiddie Kingdom and Nuka-Cola Bottling Plant(and eventually the Red Rocket station next to the park) for various reasons. I like to headcanon that under my leadership they become more like mercenary companies, since that way they help the Commonwealth while still getting to do and get that stuff they love. 

I wouldn't be surprised if Spiders manages to put something out that comes reasonably close sometime soon. They've definitely shown a clear desire (and ability) to take the issues in their previous games and use them to improve the next one. Bound By Flame improved on Mars War Logs, and Technomancer significantly improved on Bound By Flame.  I'd say Technomancer reminded me Dragon Age 2 in that it was flawed but with a lot of promise (it obviously had a much lower budget which showed, but they did some narrative and character things regarding choice that I really appreciated).  I wouldn't be surprised to see them pull off something even better with their next project.

And that's assuming we're talking production quality, if we're just talking about RPGs with Sci-fi settings like the original post asked for then that's something they've already done.

Oh, I'd forgotten about those. I was thinking about how if you went back to tell Preston that you'd done one of his sidequests, he'd always give you another one, and it would just be "Raiders in location X are bothering us."

That, aside from the railroading in the mainquest, was one of FO4's biggest shortcomings - so many generic "bad guys" with no agenda or personality besides being assholes and killing anything that moves. FO3 has some of that too, but in that game the Raiders and Super Mutants were mostly obstacles along the way instead of having tons of sidequests based only around fighting them, and in FONV, the Courier often had the opportunity to negotiate the end of some of the conflicts instead of going straight to pulling out a gun. In FO4, even the Raiders who seemed to be up to something a little more interesting, e.g. the ones running that robot race track, still just start shooting at you the moment they see you.