Would something like a Baldur's Gate style real time combat system work? Here's I can foresee it...
- Keep ships and groups of ships as well as the speed of combat relatively slow, so players have time to think and strategize without engaging into a clickfest
- Allow players to use the mouse to click on ships or groups of ships to move them to a location or issue commands
- On the GUI interface (just below the combat screen), have several large command buttons with simple commands (i.e. remember the KISS rule!) to order a selected ship or group of ships. Commands buttons are as follows:
(1) MOVE (selected ship(s)moves to a given location subsequently selected with the mouse pointer);
(2) ATTACK (selected ship(s) attack a target that is subsequently selected with the mouse pointer);
(3) RETREAT (selected ship(s) flee by warping out or leaving the battle screen);
(4) SPECIAL (selected ship(s) use their special attack or defense (e.g. breeching pods with boarding parties, fighter wings, cloaking device, etc...))
I would also recommend having an option to pause the battle to issue commands in single player games (I would prefer that option, personally -- I like time to relax to think!
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