I agree with Jalisurr; I even was going to use the same simile. They should come with "the basics" (your computer may have come with a video or sound card, although you can pay to install a better one). IFF, etc should definitely come standard on most not-low-budget ships. Remember, most people (other than the player) use their money for things other than ship mods. I don't want to be forced to buy a top-of-the-line computer every time I want a new desktop (especially if that means taking out half of the RAM and hocking it on ebay), but I don't want to buy a mouse for every new machine, either.
That said, I loved J.T.'s CTC. It was a really nice touch, but I think in general the standard way seems to work well.
Variants shouldn't be "better" than others after you gut it completely. However, it's also reasonable that a "maneuverable variant" may have better speed and acceleration, but less base mass (because there are "bigger engines" installed, although the player cannot do this himself. It's a custom job, and there aren't many people who do it.).
Personally, I think it's fine to give AI "money" outfits, especially if you are using methods like the canceling outfits trick Desperez mentioned. I.e. military corvettes like the Rebel Starbridge should already have "Port and Polish". Mod Starbridge, class E+ Executive Edition should already have the sigma outfits applied. In my mind, the polaris should not be allowed sigma additions, as they're already conceivably doing a better job than sigma could.
However, I think there's a better way than the "canceling outfits": give the modified ships require bits preventing them from acquiring items that are already factored into their stats. Pirate Valk IV can't buy sigma, because the jock who tweaked it to perfection has already made similar modifications.
This post has been edited by n64mon : 04 October 2009 - 10:41 PM