I think that the job of mod "balancing" becomes impossible if you don't start with specific ship classes with well defined ranges of attributes.
I also think this is the reason there is so much trouble on this mod with balance between different equipment from different ID's.
Now some would say the "band aid" approach currently used is best, you tweak it between mod releases or pass some unwritten rule to break a combo, break the old uber equipment, create new unbalances and it takes a couple days for some with datastorm and SP to figure out what is uber in the new mod, it takes the average player until he gets fragged by the uber setup a couple times to figure it out himself, it's exciting for a while (more exciting that a logical method from the baseline I'll grant), then when the honeymoons over everyone's complaining about it here and things get back to normal.
I for one think starting with a baseline for every class, from lf to dreadnaught so that they are balanced within their classes, then balancing the baseline from class to class is better. It eliminates or at least minimizes the useless ships that do nothing but take up space. It makes choice of an ID more about the ID RP than about the cool equipment or the advantages PvP, and it creates a sense of fair play.