That sounds like a pretty cool idea for a run (or short series of runs), but doesn't seem to solve the problem that I think your players are having. In my experience, a well structured campaign has a single overarching plot that becomes more and more evident (and important) as the storyline continues (for example, in my campaign, 'The Evo Conspiracy'). Within the main plot, you have a series of recurring themes (my campaigns: Halloweener Activity, Toxic Shamans, Disappearances, Mass Produced Shadowrunners, Gang War Outbreak, Elven Agents, Vanguard Spirits, Secret Evo Projects) that ties in with the main plot, with regular shadowrunning breaks in-between, as appropriate. As the players progress, they slowly learn that each of the 'themes' ties together in some way, eventually revealing the main plot as the campaign comes to a climax.
That isn't to say that you can't start up a new plot once the first resolves, but I tend to find that, at least the way I play, once the plot has climaxed and the players play through the aftermath, it's time to start new campaign.
It seems to me that your players feel more like they are in a serial episodic series than a movie; something that I find to be much less engaging.
This is definitely a pretty good start to a major plot though, so good luck.