Well, in some of those early stories, even when the good guys win, the villain's plot moves on, sometimes only advancing BECAUSE the good guys won!
Regarding the Shutdown, yes, the Resistance survived. Same as the French Resistance did in the early years of WWII. Just like the American troops at Bastogne did during the Battle of the Bulge. They survived until someone else could come and rescue them. Sometimes surviving is all the win you need.
Shadowrun is a bleak world, but that doesn't mean everything's dark. Even runners have ethics, things that they just won't do. Things they care about. Things they will lay down their lives to defend. And I would say that it is the darkness all around that makes those rare moments all the more brilliant.