Rockets are from Mars, saucers are from Venus.
Well, no, not really. But that's about as much as I'm going to say about the Freudian subtext of rockets vs. saucers. What I want to focus on instead is the technological implications of the two forms. Rockets have a lower-tech feel than saucers. It's what the Earthlings are trying to build in Earth vs. the Flying Saucers, it's what they do build in Destination Moon, Rocket Ship X-M, and When Worlds Collide. When Earthlings build and fly saucers, such as in Forbidden Planet, there's an implication of greater technological advancement.
Why? Because rockets are based on Newton's Third Law, while saucers imply breaking that law.
Rockets are reaction drives. You accelerate material really fast and spit it out the back, providing thrust. They are basically long and skinny because you need lots of room for the propellant, but want to keep crew space (and mass) to a minimum. Rockets are supposed to take off and land nose up, fins down, so the crew decks are oriented so that "down" (when the ship's at rest on a planet) and "back" (when the rocket is accelerating) are in the same direction.
Saucers are also oriented with their decks parallel to the ground when the land, but the direction of thrust is not necessarily down at all. They don't spit material out the bottom, but seem able to move in any direction freely. This is because they are reactionless drives, violating the laws of Newton. Thus, they have to be from a more advanced technology.
For more of a technical breakdown of how rockets work and what's different about reactionless drives, see the atomic rockets website (Project Rho.) I plan on doing something less technical/mathematical for Alternative V, because there are already fiddly sci-fi games with realistic detail, like GURPS Space. But I still plan on the rockets being rocket-like, and paying attention to the side-effects of having saucer technology.
I intended to add some discussion of mechanics, but I'll put that in a later post.