No solution comes to mind to the first issue because it's not your turn and you shouldn't be able to delay another person's turn for something that can wait until your turn. The system you have issue with is literally just the AI taking its turn and attacking you. In just about any other 4X game this wouldn't be a problem because unlike Gal Civ they restrict all of the players actions to their turn only instead of the wonderful feature of having secondary actions like planet management be available regardless of the turn order. It's like a pseudo simultaneous turn system without the issue of who clicks the enemy army the fastest. As for your other issue you mention, it wouldn't be difficult to implement a system to help the player know where the fight is. One way would be panning the camera over the battle in question and having a much smaller window showcasing the base details and allowing further options. Below is a link of a very crude version of what it might look like. I apologize for the color scheme.
http://imgur.com/a/EXfxm
So in this crude example, I circled two "enemy" ships as the contenders in a fight with yellow, of which you can see is a 6 vs 1. In theory, a line would pull away from both fleets and end with a small box showcasing the base stats of the fleet such as total beam power, point defense, and such. This is the total fleet power, and not a breakdown of individual ships. Below those two boxes is a larger box allowing three options. "Watch Fight" means you watch the battle as normal, "Auto Resolve" is the quick combat (I'm not sure why I didn't just type quick combat instead), and "Expand" will open the full details of the fight, showing you the window that you have issue with. With this, the player can expand that massive screen window showing all the individual ships that are partaking in the fight if they so desire.
Some other notes is that the player cannot pan the camera away from the fight when this event pops up, but that can mouse wheel scroll, allowing them to zoom out and see where in the galaxy the fight is taking place in case the local area doesn't seem familiar to them. Additionally, instead of an ugly yellow circle surrounding the two opposing fleets, there would be a highlight of some kind that clearly indicates the two tiles in question, so in the event of having multiple fleets adjacent to each other the player will clearly know which two tiles/fleets are fighting.
Again, this is a crude example, but maybe that concept would make it easier for you to know where fights are happening and allowing you the options to know the finer details of the battle, or simply auto resolve and continue on. In theory, this concept would be less jarring as the players don't have this massive black screen of the fleet details just popping in front of their face, which makes it easier to stay immersed on the galactic map.