The majority of US equipment is built by the lowest bidder. But, the equipment must meet or exceed a set of standards. Failure to meet the standards on one item can result in the company loosing all of its military contracts, having them awarded to competitors.
As an example, colt manufactures the m-16/m-4. When the military started looking at a replacement weapon that had a sealed gas return system (prevents fowling from gunpowder residue, reducing failure rate), Colt responded that they could do that too. Basically, their defense was that it wasn't in the standards for the weapon to have that system, if the army wanted to add it to the standard colt could still supply weapons.
Ships do not normally fit into this category. Sometimes a competition is held where competing shipyards submit designs for a new ship. Once a ship design is accepted for use, the yard that designed the ship builds the ships based on that design.
Even though the yard designs and builds the ship, it often buys components from other manufacturers. Installed equipment, and this includes weapon systems, are purchased from other sources.
I can certainly see Features and Flaws related to the procurement process, but a few of them already exist in the Vehicle manual. Quite a few of the features could be specified by a military (spacious being the exception). Many of the flaws could be seen on a ship that was first of it's class (a new ship design), some of those would be corrected on the lead ship, and there would be redesign to try to remove them all. Some that would be considered designed flaws (they were used intentionally rather then accidentally) are: Cramped Cockpit, Exposed Weapons (may only apply to certain systems), and Planned Obsolescence. There's a few others that could be designed flaws.
If a government has control over what a military acquires, individuals in the government often seek some advantage. This could result in a number of flaws. That's not to say that when the military has a free hand that it does so effectively. One of the contributing factors to Germany's fall during WWII was that different generals had their troops outfitted with weapons & equipment that competed with and was incompatible with the equipment of other generals troops.
Bureaucratic Wrangling: at least one component or system must be manufactured by a company that produces an inferior but more expensive version. Choose a system & multiply cost by 2.
Quirk: the system still meets standards;
Minor: system barely meets standards;
Major: when under stress, the system may fail;
Greater: the system has a hidden flaw that could threaten the ships survival. Revelation of the flaw could threaten lawmakers, military leaders, and company, which may result in a cover-up (witness' would be troublesome, but accidents happen in space all the time)