Perhaps I am a little late with this suggestion, but would be great to be able to toggle or hold to invert hotkey for "Enable weapon control" option, so let's say you have it on, then you do Alt + click on enemy ship and the weapons you have currently selected target enemy ship independently, or it can also work the other way - hold Alt to manually target your weapons (maybe even in non-direct control mode?).
PS: the update feels absolutely fantastic and opens so many possibilities, the only thing stopping it from being game changing is the usual 2-3 and sometimes 5+ second command delay on multiplayer matches.
Also something that bothers me a little in multiplayer with direct control - it seems like your weapons target the place server thinks as to be the mouse position and the result is sometimes stuttering position location when ship is moving, would be lovely if client would tell the server mouse position relative to the ship instead of to background, that way sudden stutters wouldn't lock the target position in place. It is most noticeable on prisms.