The devs could make all systems 'confed systems' but then all systems would have the same ship ratios. If a better method is implemented, then by all means, axe the factions.
Spirit, if the purpose of classifying bases by "faction" is to regulate ship ratios, maybe Brad's concern might be addressed simply by removing the lables. After all, if I go to New Detroit and see mostly merchant ships, I'll think of New Detroit as a merchant kind of place, without the need to have a "Merchant" lable in my HUD. In other words, make the "faction attribute" a hidden attribute. I'm sure Hellcat can give you a quick patch to have the lable removed.
Going back to the (jump) point: I agree with you that blue balls look goofy. Maybe I shall use a stronger word: "unscientific", unless there's some reasonable explanation somewhere in the literature. That's why I thought that gates, like in P2 might make more sense. But I realize that this would be too much of a departure from the tradition. So let me assume that the technology to open a wormhole is contained within the "jump drive" alone, and that what the jump drive is doing is precipitating an opening of "hyperspace", but can only do so at locations where hyperspace is very close to normal space. Now, the purpose of the buoys or bubbles is to identify those locations for traveling ships.
Now, then, we could say that the location could be marked by an external object, such as a buoy, or simply be triangulated by your ship's computer. There are many references in Privateer to jump-points being "programmed" into the ship's computer, by the way. These two methods could overlap.
Now, the bubbles:
The bubbles could just be artificial projections of the ship's computer onto the HUD. Now, what IS an HUD. In fighter planes, there's a piece of glass tilted at 45 degrees from the vertical, with a CRT display flat on the dashboard, under it; such that you see the reflection of the display image on the glass, as if it was overlayed on top of what you see in front of you. That way, a box can be drawn around an enemy plane, when you have lock, for instance. So, if the ships in WC or in Privateer have an HUD, the computer can project a (goofy?) image onto the HUD, just to let you know that's the place to fly to. In which case, some ship computers might project it as a blue ball, some as an orange cube, or whatever.
Makes sense?
If we were to adopt this policy, we'd need a little engine patch to make the blue balls NOT show up when you're looking through the side windows, or from an external view, though.
As for buoys, perhaps the military prefers to have physical markers as a back up, in case a ship's computer has been damaged, and the pilot needs to make it back to base by eye-ball.