Freespace 2 is no different.

If the mission has lots of combat or it makes you do stuff all the time there is nothing you can do but if there´s a long wait or if you just know that nothing is going to happen you can accelerate the time by pressing "SHIFT+." and after that slow it down with "SHIFT+,".

It's the same in every space sim in the era, isn't it? Actually I think it is better without checkpoints. When you're on the final leg of a long hard mission, down to 5% of hull, you really feel scared! Your palms sweat; your heart races. Those are some of the most memorable moments. One such experience is blowing up and escaping the second Death Star in XWA. Oh, and blowing up planet Kilrah in Wing Commander 3.

I think Halo might have popularized the checkpoint system. I have to say I was never very scared in Halo or CoD or any checkpoint-filled games, because if you die you only lose a few minutes and then there's no other consequences.

Back to topic, I think the worst thing in FS1 was the lack of interesting cap-ship weapons (beams, flaks). Made the big ships boring at times.

There's checkpoints in the Defiance campaign for I-War, I have to say I enjoyed not having to repeat the easy parts of missions to get to the hard parts.