I like the single book missions, for the reasons David stated above. Much more than that and you run the risk of going X-Files. That is creating a monster you just will never be able to satisfactorily wrap up. I'm not a fan of the big season or inter-season long story arcs on tv either.
Plus you get something new each time.
Its sometimes good to have long story arcs if there is lots of action and less talking. Plus long missions makes the novel interesting and noticing conflict between commanders and being commanded. The only thing I hate about long missions is that you have to wait for the next book to come out which takes about a year or so.
For example, Dragonball Z (anime) pissed me off because they talk for the entire episode and fight for two minutes then talk some more in the next episode. I can't stand that.