Having a large number of exceptions to ships (this is the third 'exception' ship in the earth alliance) is a problem for most gaming systems. Exceptions are very hard to balance, especially when there is no limit to the amount of exceptions you can have in one fleet.
The Earth alliance in the Crusade era could concienably field a Nemesis, 3 Apollos, 2 Chronus and 2 Delphi. A fleet where most ships require additional thought because you cannot just ask the traits, you have to know the ship. Strong anti-stealth fleet as well, would the Minbari still be balanced against it given all but the Chronus can 'fit out' for anti-stealth work? Hard to say.
I do not think that what we are dealing with so far is bad, but I find the idea of more and more of these 'notes' on ships to be an almost inevitable problem. We are already adding layers of rules, FAQ, errata, to a game that has as one of its big marketing points simplicity.
One of the big reasons I was against the Aux craft/fighter vs ship distinction. Would be fine if each had a seperate section in the rules describing how they move, shoot, take SAs, etc. but the way they have structured the rules is to say they are just like ships but... Its a format that screams for misinterpretation, overlooked assumption (enemy fighters or more than four fighters on a base anyone) and unintended consequence.
When you write rules keep each rule clear, concise, do not share terms between similar rules, and above all do not make more than one exception per rule. Otherwise the exception becomes the rule and folks are always reaching for a book and going 'how does that work?'