Most games deal with the cool factor becoming tedious by giving you both options. At first you have to do everything manually cause your tech/ship is basic. But as you upgrade, or run into melnorme traders you eventually get a landing computer that does it for you. While still allowing manual control if necessary.
While the Ur-quan themselves were "busy". They did have battle thralls for that sort of thing. I was not talking about the destruction of earth, but more to make sure none of the earlier alliance races were supporting the humans.
I think the fact that humans were sort of a side story in SC2 was what made the story so powerful. It wasn't humans that were going to build up and free the galaxy from the Ur-quan. It was the lost colony of humans sneaking around and forming Alliances/black market deals to free the Chenjesu who would come up with a plan to defeat the Ur-quan. A few areas where the story lacked coherence was that as soon as the Ur-quan found you, they should have bee lined for Earth
Rebel Galaxy did everything in isometric view. It was not hard to aim in that game. As a matter of fact aiming was a matter of skill and was a mini game in its own way. It gave a lot of good tools for tracking your opponents and dodging attacks. The only thing with isometric is that the camera has to be perfect or it ruins the whole experience. It has to be quick, allow for a lot of zooming quickly, and be able to track targets or weapon arcs. Isometric usual
Having the ability to see the solar system at a glance is a must. I also like the close up view of your ship and planets as your traveling too. I think pressing the spacebar(assignable button) to go to a solar overview where you can see everything in minimalist view, then press space to zoom in would be perfect. The ship needs to be controllable in both screens.