Some of the points I made earlier I should clarify - keep in mind I love long games - over 100+ system maps most of the time. My early game definition is typically the first 400 turns. In Sword of the Stars I, I viewed the first 100 turns as "early game." Things have changed and this game takes a lot more management and planning, than the first - a good thing in my opinion, because I play the game because I like the challenge and the planning needed.
A defensive fleet for every system is expensive, but it would be even more expensive imho to have to rebuild assets (heaven forbid re-colonize) that could be destroyed when a system is attacked without any defenders - stations, especially upgraded ones - which is how your mid game and late game should have to maximize your benefits take money and time. If you lose a level 3-5 science station, it will not only cost money to rebuild and rebuild all the modules you have invested in, but time, a long time, because you cannot upgrade them as soon as the station is built. Think of this time as lost potential, your construction fleets (you do have more than one right...?) should be moving with your frontier for the most part building new stations rather than having to rebuild old ones.
Stations - I see no point in doing things half-way. I see the early game as your build to the mid to late game, invest early, defend your investments and then allow them to pay off for the rest of the game. I think the ideal should be to have your stations upgraded to maximize your benefits, for example, with science, I love to research everything possible, but I prioritize what I need first, so in my ideal game, near the end of the mid game, I will have one science station for every tech tree branch and most of them upgraded to max - this makes research that much faster, especially when you need it.
More points later...when I have time.
A good plan, violently executed now, is better than a perfect plan next week.
George S. Patton, US general (1885 - 1945)