It didn't help that they switched game engines part way into development and had to start again for a fair portion of it. I believe thay started with Quake1, but moved to Quake2 over time (A good choice IMHO).
My understand was that the game was origional not to have a sequel but be twice as long, things got rushed towards the end to close the story off and release it to shelves.
Don't let that put you off though. It might end a little abrupt and on a cliffhanger but its a self contained story enough to play through.