It would have been really cool to get a cutscene similar to the launch of Cryo, like an ONI transmission having the factions chime in about the discoveries in Cryo.
We could still be getting that I hope, just delayed reaction.
Similar to when a Destiny fireteam completed a raid for the first time and they dropped everyone a cutscene in Orbit, but this would be exclusive story interaction for the crew that actually faced the Compiler.
In hindsight, ONI or even Arachne could have given out a new cutscene/Priority Contract for all runners after the world's first Compiler kill, pushing more crews to do the same.
The codex says information on the mysterious entity will be developed further as runners get more info, I think S3 was always meant to be the next story addition while S2 was a buffer as we were getting VA teases for S3...but I agree it was rough to not have any real new story progression as that's a big hook for me.
I think the upcoming social space could be a really neat way to have some form of social story happening there too.
Since NONE of the Factions have any reaction to the Marathon, Cryo, the Compiler or Durandal, whether intentional or not, it tells the audience they don't give a damn. Yet we KNOW that's not true!