All is not lost story-wise.
I personally believe that the ability to create a storyline is quite important for FPSC, and easy to do to from Lee's perspective (so assist me with the joint pestering effort after the EA release!)
FPI scripts, which are used by enemy AI can run other scripts and they can play sounds, so you could create a storyline Half-Life style by playing recorded speech when you approach a character. This would require manually editing the script of course, but I'm sure an automated editor could be created for that.
In addition, you can edit all of the media in the game, so you could create a storyline in a slightly more subtle way (the way that Half-Life 2 created a big-brother feeling by having faceless enemies, panicky civilians and mysterious blood-stains on walls for example)
The HUD itself is scriptable so it might be possible to display 2D graphics on screen.
BlueGUI Windows Plugin