While it would be chaos for managing, it would truly emphasize the use of the empire/fleet management pane on the left of the screen. It would also make use of the hotkeys more frequently.
An optional game-setting would be awesome.
If you have played SimCity, having such actions would be a form of pathfinding. Pathfinding is intensive on the CPU. With the majority of the people out there now sporting i5 2500k's, that would not be an issue because, lets face it, those CPU's are beasts!
By all means though, SimCity games continue to stress modern CPU cores still. They have to concurrently process the movements of MILLIONS of individuals at any one second. Having ships as one big entity, and a fleet of 100+, well, that'd only be 100+ things to process rather than millions.
AOE's is an issue as well, yes. There should be a button or two in the ships panel to tell them to follow a certain group of targets. Or, if a ship passes into the AOE and out of it, the effects could linger for a few seconds after the run and they'd slowly get weaker and weaker the further away the get from the AoE. That way, there wouldn't be a strict AOE limitation where its you are either in it or out of it. The further away you are from it, the weaker it is.
Indeed having the devs implement something like this would be challenging, but for people who love realism and eyecandies... It'd be greatness! The programming required for ships to dodge things like asteroids and planets would add additional bulk, while ships pass one another in gravity wells.
I think it is quite possible. If you have played Sword of the Stars, something similar goes on in that game... But those battles are limited to 5 ships at most on each side.
As a personal note, I should add though that I am a micromanagement wh0re. Anything relating with it... It will consume me until I master the techniques (or economy).