I have been having conflicting feelings about the changing focus in the main screen also, and not just with battles.
If I check the option boxes to watch my autopilot moves (and the enemy moves as well) I think that I would like the option to have the game pause, after each ship move, before flitting off to the next ship to move. That would let me see the results of that ships new discoveries. Then after hitting a key (space bar for example) the game would continue on to the next ship.
As it stands now the screen jumps around so quickly that I can't see what is happening and have to check through each ship by hand afterwards to see what happened. Did my survey ships find any new goodies? Are my autopiloted ships passing anything of interest? Are my autopioleted ships indeed still moving (Beta versions only)? etc. etc
When I am moving many ships about for various nefarious reasons it is almost annoying to have the game automatically jump to the next ship it has in its list. It more often then not breaks my train of thought.
Maybe the option to have to choose the next ship by hand would be better. For example, if I have a few ships (or stacks) in one area I would just choose the ship to move by chosing it and giving orders. If I am finished with all the ships that I can see in the main window I can just hit the "FIND" key and contunue from there.
It is almost like I would like the option to disable all the automatic focus changing that goes on.
Maybe it is just my inexperience with the game, and as I get more familiar with the controls I will see the error of my ways, but currently I am often confused by what I am looking at.
Elrikk
PS I sometimes wish that the Main and Mini maps could be switched by hitting a key. (or having a zoom on the main map too) This would probably cause to many problems though, with the sizing of the ship icons.
I am really enjoying the game though.