I know about all of the legal precedence; this isn't the first copyright product I've worked on during an unofficial prototype phase. My desire is to make a working prototype that is enjoyable (a remarkably hard feat, truth be told). If I am able to do that, then I will shop licensing and corporate interest. For example, if Toys For Bob has the rights to non-electronic media and shows interest, that is a route. Conversely, should Stardock want to start a ground swell of interest to seed the path for a new game and are legally able to do so, that is an option as well. Finally, as you very correctly pointed out, if all else fails, we call it "Solar Oversight" and make it a spiritual successor.
Regarding non-player controlled entities, such as the DOGI, Ur-Quan Fighters, Orz Marines, Syreen enthralled crew members, Earthling Missles, Korh-Ah blades, Mycon Plasma (and many more), we have some very simple rules in place. Each of these items operate independently of the player once they are "spawned" and all of the interactions are thankfully rather simplistic; normally boiling down to, "progress towards target like a heat seeking Missle", "Sit still", or "head straight until told otherwise" (or some combinations there of). So, for current testing, we are considering all of these spawned items "Projectiles".
Since the game is currently a .5 turn-based style (that is, players play at the same time, but there is an order of operations for resolution), that gives us a "Projectiles" phase after each player action where the projectiles "AI" performs their own action. The Earlthling Nuke moves two spaces towards the opponent, exploding upon reaching the opponent or exploding harmlessly after 4 moves. The Ur-Quan fighters and Chenjesu DOGI move towards the opponent 1 space per action and, at the end of this movement, if they are in the same spot they perform their action (doing damage or reducing Batt).
This makes all "Projectiles" living parts of the combat ring that players have to consider and manage, but never make choices for as they autonomous. Also, since it's all on the ring (and therefore 1 dimensional instead of 2 dimensional like in the game) there is not time sink in decision making or arguing about turning radius or anything like that. I think this will keep the game much more accessible.
The only two that will make this battle system a bit harder will be the Chenjesu and Kohr-Ah Primary attacks as a big part of their perfectly straight movement is predictive targeting and player control. Admittedly, I haven't worked that out to a point that is satisfactory yet, but one hurdle at a time. If I can make a system that makes all the other ships feel "good" then I can worry about figuring those out later.
As for the current tracking, I am using simple tokens to denote position on the battle ring. Here is actually a picture of the assets I printed for the first prototype test! http://imgur.com/HlUkY4O
These are super rough, and the numbers are WAY off, (and the nukes are too small), but those are the assets I'm currently using. Yes, those are little Lego Ur-Quan Fighters. They are brilliant, and totally just something I found on google image search.
Also as a shameless plug, I plan on streaming Star Con 1 & 2 on the company twitch channel as soon as I get my computer updated in a couple weeks. If you don't mind watching someone absolutely suck at your favorite game, you're welcome to stop by. https://www.twitch.tv/bsdover