The Freespace Universe is a big place full of ambiguities and often conflicting information. In its current dormant state, there is no official source for updates or corrections easily accessed by its fans. In one's own fanfiction, one can write any changes one wants. Is it canon? Not unless the official creators actually return and validate the material.
Until such time as the devs decide to revive the franchise however, the information that has been officially released is the last official word given, and without them around to approve or disprove changes, it pretty much should be taken at face value, even if it offends our sensibilities on the 'Way things ought to be'. Without an official interpretation of the issues, anything else is supposition.
When writing, a lot of folks don't believe in letting canon get in the way of their vision, and that is their right. I personally don't get bothered or upset by this, although I much prefer fan made works that keep within the boundaries of the canon. It is more enjoyable in the greater context of the gameverse for myself if the player made acontent can stay as near as possible within the canon for consistency rather than creating the need to rationalize out any newly introduced plot issues.
My personal feeling is that the Ancients were very widespread and extremely advanced, just not able to combat the Shivans effectively. Their megalithic subspace portal technology alone shows they were quite advanced in both construction and technology, also that they had the resources to apparently commonly construct these devices - three were encountered in the main campaign. Not only that, the devices themselves were quite sylized and decorative, not merely built for function. They obviously weren't shy about the investment in resources to build them as desired. This is plenty of evidence to indicate that the Ancients were likely very widespread indeed. To what extent? That part remains somewhat undeterminable.
