"Retool time" is probably more realistic, but Aurora already has enough stuff that could be considered micromanagement, making it worse would probably not be a good idea. I like the idea of general IC's, and the ability to build more than one thing at a time, but you already are including specialized factories for fuel and maintenance production. How about dividing IC's into Heavy IC and Light IC. Light IC would be used for missiles, fighters, and ship/PDC component construction, and Heavy IC would be used for everything else. That way you couldn't concentrate all of your construction capacity on surge-producing missiles or fighters, and in any case it doesn't make sense to say that a factory producing heavy industrial tools for other factories one month can be switched over to producing missiles next month, or at all. It wouldn't be too much of a stretch to say that such a factory could be converted from producing heavy industrial production equipment to heavy mining equipment, but it is a much bigger leap to producing intricate electronics like missiles or fighters.
I agree that retool time would probably be the most realistic but as you say, that would involve a lot of micromanagement and the realism gain probably isn't worth the gameplay penalty.
The Heavy/Light IC is an interesting idea. It is similar to the idea of restricting the missile/fighter percentages but it would also restrict the heavy industry percentage, although I am not that bothered about restricting heavy construction as I don't believe that would cause a balance problem. My concern is that I want to try and streamline the construction into a single interface with a single overall industrial capacity and Heavy IC and Light IC would lie about halfway between the current situation and the one I am aiming for. It would effectively combine fighter and ordnance factories but leave them separate to construction factories. I also mentioned the idea of converting industry from fighter/missile to heavy in a post earlier today, which would result in similar mechanics to the Heavy/Light concept. After further thought though I think that using that mechanic could cause some issues around the percentage allocated to each construction project.
I went for the concept of a percentage of industrial capacity allocated to each construction project (as shown in the screenshot in the earlier post) so that adding IC or removing IC from a planet wouldn't cause problems with existing allocation. The other option was allocating a specific number of factories to a particular project but in that scenario, removing factories would require a decision on which projects would be affected while adding new factories would result in unallocated capacity, both of which could lead to micromanagement. With the percentage concept, you can add and remove factories without worrying about existing allocations to projects. However, with a light/heavy concept or a conversion concept, the problem would return as you would have to specify whether you were adding/removing heavy or light. Within the overall percentage concept, the mechanic of restricting the total percentage you could dedicate to fighters or missiles would effectively create a section of light industry. The non-fighter and non-missile percentages (the heavy industry) wouldn't be able to produce fighters or missiles. The reverse wouldn't be true as 'light' industry (the max percentage that could be dedicated to fighters/missiles) would still be able to carry out 'heavy' tasks but that is far less of a concern from a game balance perspective.
Steve