Well the reputation portion is sort of being done in world of starcraft 3, and the whole "command the computer's units" thing HAS been done before somewhere I cannot currently recall. However, you can probably do a better job of the commanding computer units than whoever did it before, and your reputation system is fairly unique, as WoS3's isn't really all that similar, just the same name and a few similarities.
Some problems you will probably encounter
- Micromanaging units not under your control requires a "virtual curser" which makes it highly unweildly
- As the units increase in rank they don't necessarily get better, a ghost ranks higher than a marine yet is worse in straight combat (Modifying stats would fix this, but makes it loose the "feel" a bit)
- If it is multiplayer, you're going to need a whole lot of computer players.
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Virtual Curser: Yes, I know, its a downside. The units will be set to automatically defend the area they are at, but making specific commands may be a problem.
Rank: Units will be edited to make it so that they actually will be more effective as the rank goes up. For instance, a battlecruiser really shouldn't be so weak as to be taken down by 7 marines, thats just silly. Small stuff like this will be fixed.
Multiplayer: Oh god, don't even remind me...