Random CQ is fair enough for campaigns, as noted it helps the 'character' of the fleet. However, in one-off games it can really matter.
It was never much of an issue in the original ACTA, as a disconcerting proportion of criticals couldn't be repaired and most of the special actions you gave a damn about were automatic.
Now, however, CQ is genuinely important.
I'd go with a simple rule for tweaking ships - either assume your fleet is all military-grade (CQ4), or it's a mix. If it's a mix, you'll get newly established crews and ships just out of refit as well as grizzled veterans. As such you may increase any ship's CQ by 1 or 2, but for each ship's CQ you increase you must decrease the CQ of another ship which is no less expensive (including the cost of options such as command variants) by the same amount.
i.e. if you have a squadron of 6 D7s, you can make one two-ship division veterans, but would have to make another two CQ3.