so you somehow must go around that obstacle.
How? If you make the shivans not-node dependant (give them some portable portals, super-jump drives or dimensional rifts) then how the hell would the GTVA stop them? Making the GTVA superior and actually defeating the shivans is...well..
See: Derelict.
Frankly, Shivans becoming a big threat post-FS2 isn't difficult. It is trite, however, to have a campaign that says "lol the destroeyrs haf retunred we will kill them oh no we r screweedd lol." Having the Shivans as rampaging destroyers who are aimed at the complete destruction of the Terrans and Vasudans really does get old after FS, FS2, and the countless FS2 mods related to the return of the Shivans.
To make it interesting, one typically has to make his own rules for the Shivans, or really stretch some details from FS2. For example, giving the Shivans something to be afraid of, such as another, larger race, adds something interesting and a plot twist to a new campaign, but violates what we can deduct as the Shivans being the Great Preservers; now, instead, they are a terrified little race of bugs that has a giant can of Raid aimed at them. You can stretch some things from canonical FS, such as the Ancients not being entirely wiped out, ETAK being used to manipulate and control the Shivans, or the Shivans not being the race that had wiped out the Ancients.
Basically, what we know about the Shivans restricts creativity along canonical lines; we're told the Shivans are a race that destroy spacefaring races when they go too far, and will relentlessly pursue their goal. Unless someone can add subplots or other facets of the Shivans that would make this interesting a third time, I think we may be at an end of what we can do with the Shivans so far as a full-fledged campaign is concerned.
This doesn't limit historical campaigns, however. Having a campaign set during the FS/FS2 timelines is more acceptable, seeing as how it doesn't create a Third Great War, but simply elaborates on the first two.