So one thing I've run into is that as your fleets get larger your combat formations get less and less optimal. While whatever algorithm is setting up your ships does a good job of putting vulnerable stuff like transports in the back and escort cruisers up front, it also pushes the left and right flank ships forward of the main formation, which makes it tough to defend them against giant missile swarms or the like. It would be useful to be able to place ships were you want them before the shooting starts, particularly since in large formations actually moving ships around can be problematic. So some sort of pre-combat step that allows you to customize your formation would be appreciated, with some ability to 'remember' your setup so you don't have re-tweak it every time.

-Will

I second this.
Also it puts (very nice) military transports at those (vulnerable) front side positions. After all they are armed only with missiles - what good can they do in the first row?

If we cant get that, at least see if there is a simple way to put escorts out front. I spend my first 2~3 turns bringing up my CLs and DDs to screen my CAs and BBs before we can start marching forward.