How far are you going to go with the new AI routines? One thing that (in general) annoys me with AI is the "All or Nothing" approach. Once an AI has set itself the goal to conquer an object or destroy a certain target, it will not deviate from that if initial plans fail. It just begins pumping more and more ships and resources into the set goal; rather than a human player who would at some point see, that he looses his long term goal, when he continues that way.
Also in ship-to-ship combat. At some point human players realize that it would be better to withdraw from a certain position and take the loss of a space station or a planet in order to preserve the fleet, which could be very usefull having it in a different combat. Meaning, it would be worse if there is no fleet but still have that one planet or space station.
Will the C# AI be able to alter its goals depending on such circumstances?
The AI will assess the situation and determine if an attack is a good idea. If the AI does not believe it can win a fight, it will retreat or not engage. It will start withdrawing unarmed ships from systems near any threat and if hostile forces are in the system it will choose the least threatened route to run (one AI function is actually called PlanEscapeRoute). If no good way out of the system exists, the AI will move to the cover of a defended population if possible.
If the AI chooses to fight, it will deploy accordingly. A single hostile ship might only attract the attention of a destroyer squadron while any NPR battle fleet remains at a strategic location. The AI will stage forces before launching a major attack and will not approach piecemeal. It will also decide if certain locations need protection and if that is more important than attacking. The major difference for C# is that there are Race, System, Fleet, Ship and Population AIs that exchange information and make decisions at different levels. In VB6, each fleet has its own directives and these are often not coordinated (although escorts will attempt to protect other ships for example).
I haven't coded this portion yet but the AI will also learn about your ships through observation and estimate their threat level, strength and defences based on that observation. Those estimates will influence its actions.
Although it won't be a good as a human, the C# AI should be significantly better than in VB6.