Technically we will not include Fred in the download itself, but everyone who want's it can get it over at HLP. It's a little difficult because of the mass of beta-release builds, so we decided not to include one, otherwise we will be most certainly overwhelmed by support-questions about SCP instabilities (which doesn't mean we give no support at all, but I think for fredding-questions HLP is the better place.).
But I would like to point out, that at the current point of development we still use an older SCP-Build for our game, because it's pretty stable. But this also means that new Fred-Builds will not work with our table-files (those are the freespace configfiles). On the other hand, it's not such a big deal changing them to work with the new builds, so anyone interested will be able to do this really fast.
To answer your question, technically you can do almost everything with the Fred-Editor. It makes the briefings/debriefings, ingame messages, autopilot and so on. The new builds even support creating cutscenes using fred-scripts and the game engine. The possibilities to script are numerous (to say at least).
Starman