Shadowrun returns was amusing, but yeah, I was looking for quest variance. Although for a modern successor to Black Isle's games, try Age of Decadence by Iron Tower (they also have an upcoming sci-fi one). The things lives, eats, breathes, dies, and resurrects on choices, consequences, and branching interactions. That was the title I actually had in mind when thinking about a 2D Cyberpunk '77.
Take an example early mid-game quest, go to the Mine guarded by Other Faction to get the MacGuffin. You can (provided you have the skills and build)...
1. Imitate an academic, made easier by possibly interrogating the real academic who was supposed to go there and acquiring the appropriate accoutrement.
2. Actually be an academic who can talk with confidence about MacGuffins, ending up with you working for someone else and completely re-routing the plot.
3. Sneak in and steal it.
4. Arrange for poison to be delivered in the guard's supplies by persuading/initmidating/bribing the teamsters. Acquire the poison by buying local rat poison, convincing an apothecary to sell you the good stuff, or make your own at various levels of efficavy based on your skills...which directly translates to the garrison being sick and an easier fight, vomiting horribly and a much easier fight, or mostly dead.
5. Talk to the guard captain, then stab him in the throat while chatting to kick off the fight.
6. Go hire a bunch of bandits you need to deal with on another issue to come and take the mine for you, solving both of your problems in one swoop.
7. Represent a local noble and inform the mine guards that yes, they would probably kill you in a fight, but that would give said noble the pre-text to come here with a small army, kill them all, and take it anyhow.
8. Actually just storm the damn place as a one man army (Hard. Very Hard.)
You can't build that sort of functionality into big 3D open worlds, not at a reasonable price point. But bloody hell would it make for great cyberpunkery.
Wow! Now we are taking. Haven't heard about this game. After I finish F2 (Sierra Army Depot atm) I will definitely play it. Sounds impressive.