OK just started reading it and here the first couple of notes about the introduction (as I have time, I'll read the rest of the document too and give my feedback).
Strife is definitely not the first FPS-RPG crossbreed. 1994 saw the release of ShadowCaster, an FPS-RPG crossbreed using a heavily modified Wolfenstein engine.
The greatest mistake of Rogue was to take too long to release Strife. DOOM was released in 1993 and Heretic in 1994. Strife was released in 1996, at a time when the first new generation FPS, Quake, was already out. At that point of time, interest in previous generation FPS rapidly fell.
The source code of Strife is allegedly lost. James Monroe, who's been working for Raven Software for ~6-7 years by now, was the lead programmer on Strife and when I once asked whether he could give us the source code now that it ha no commercial value any more, the answer was that he doesn't even know where it is if it's still anywhere at all.
There are many possibilities that might backfire, but AFAIK none of the choices really result in your not being able to get through the game at all. I found one thing though that's not very obvious and still means you have to restart the game from the beginning: if you kill that annoying thug in the town hall before getting access to the rebel base, you'll never be able to get in touch with the rebels and proceed in the game. Once he opens the door, you're free to kill him though.