The career agents are terrible. I have done them far too many times, on far too many characters, because they give out a lot of free crap. But they are obnoxious to run. They have a bit of a story to them, but the thing is, the rewards that are supposed to be given out are all weird, so you go into a mission given a specific ship piece in the last mission that doesn't help you at all on this next mission. No, you need to go and train this completely unspecified skill so that you can fit this other module they mentioned nothing about until right this very moment.
I was given a remote repair frigate while I was doing the exploration one I believe? I was not given probes or a probe launcher, I had to figure that out myself.
The one with the most storyline is probably the military one, in that one the pirate says to you at the end "you know, you can work for the pirates" but that about sums up the depth of the story. The other tend to have less then that, though I think in the advanced military one your agent was fucking with you a bit.