Is there a preferred way to move through the 'Sector Map'?

Solution 1:

Generally, hostile sectors will have more combat encounters, while civilian and nebulae tend to have more story-driven encounters. Many events in nebulae have outcomes which depend on having a specific system on a specific level, so they favor generalism over specialization. Civilian sectors have the most shopping opportunities, so when you have a lot of scrap to spend, you might want to fly through a civilian sector. But these differences are not that large.

But it's not just the color which is relevant. A far more interesting information is who controls a given sector, because this determines which events and enemies you will encounter. Depending on where you place your focus while upgrading your ship, it might be more or less fit for certain enemies and events you will encounter. Also, when you want to unlock new ship designs: Many of them can only be unlocked through events which only occur in sectors controlled by specific races.