The fleet size option should not have anything to do with it, because the capital ship and supply are merely researches. I could easily add or change them without concern, and there is no reason that would effect it. If something does not effect the rest of the Research trees there should be no reason why it should effect the Fleet tree. Do not think that the way the fleet tree works is somehow different then the noncombat or combat trees, or you will be quite mistaken.
Also, before I did not mean tweaking the AI, as I do not plan on messing on anything hardcoded. At the beginning of the game, each computer player is assigned a different profile on what it should take priority over other things. Much like in the galaxy file, which assigns certain planets to spawn more often then others and can be modified, so can this file. Basically, I am not changing the AI, I will be merely changing what these profiles mean toward telling the computer what to take priority over another. I cannnot remember the name of the file at this time, might be the constrants file but I cannot be sure as I cannot look for it being away from home, and my hangover has blurred my memory.
I know how the AI works with new research more then most people, as I should. Other then the graphic mods and the files from Sins Plus, this mod is an original piece of work written by yours truly, and as far as I can tell something no one has done other then me. In my opinion you are overthinking a minor problem, making it seem greater then it really is, perhaps because of a lack of understanding on how it works.
Anyhow, I will be getting back home later today and I will take a look into it.