Q: So a universe of faster-than-light travel favors surprise attacks?
A: It really, really does. You can go and mug somebody and they never see it coming. Of course, not all faster-than-light drives in fiction work the same way, but the Cylon drives certainly had that attribute.
Q: You have a list of factors that real navies must contend with, such as doctrine and acquisitions, that sci-fi navies don't. Can you elaborate?
A: The full-up list is pretty long, but the different pieces group nicely into six major areas: 1) strategic assumptions, 2) strategic goals, 3) fleet missions, 4) fleet design, 5) force size, and 6) force management. These are the sorts of things one needs to think about when designing a navy. Most science fiction does not cover the whole model; at best it might cover Fleet Missions and Fleet Design in detail, with most other areas only vaguely defined.
Another issue is that modern naval warfare is very much tied to a logistics. There is a lifeline to the shore, and on top of that, there is this support network across the world, such as satellite, meteorological support, and land-based aircraft. Air campaigns are planned ashore. This idea that Captain Kirk leaves on a five-year mission? We go to sea for six or nine months at a time, with continuous logistical support, and when we come back, the ships are pretty beaten up. They need refit. It's hard to imagine these spaceships going out alone and unafraid without any sort of support. Most sci-fi authors ignore that, and haven't thought about what would be needed. Interestingly, the sci-fi authors of the 1950s were better at thinking it though. It was a time when everyone was talking about how a hydroponics section would be needed to provide food on a starship. Maybe nowadays you can say you have a magic power source, or nanotech to produce the materials you need. But I really get the impression that sci-fi doesn't really understand this stuff.