The problem is that if I want to pick up extra mk versions of the flagship I do it to it's direct combat abilities which are nice, not the munitions boost which I think is great for a free ship, but terrible to upgrade due to munitions alone.
I guess what I mean is I wish it's munitions abilities scaled better with cap with the acceptance its direct combat abilities would suffer. Right now I think of it as a zenith ship (because the two share so many bonuses, oddly enough) except it sacrificies an addition bonus damage slot in return for munition boosting. Pretty sweet deal for a mk I, not nearly as sweet for the mk III.
To put it in a third most concise way: The mk I munitions is awesome, the mk III muntions is terrible. I wish it followed the military comm lines of increases, where if the mk I had 40% the mk II would have 100%, and the III 200%. Even if the flagship lost all its bonuses to pay for it, I would use the flagship more for it would truly act as a flagship, not as it currently is as a slightly more frail zenith starship that also provides muntion boosting.
It's hard to describe...but I'm trying to say the flagship and zenith starship feel too alike, with exact general dps (flagship actually stronger due to fewer shots and armor piercing) the two sharing so many bonuses, with the only point of contention really being do you want 20% more hp with the zenith or 40% munitions boost with the flagship when both are mk I.
EDIT: What a clusterfudge of a post. I'm trying to say 40% munitions for mk I is awesome, but 100% for III is terrible, yet military stations seem to get the numbers right. Simultaneously, I am saying zenith and flagships feel too samey, and that the flagship should be nerfed in dps compared to the zenith to help balance my desired increase in II and III munitions boosting.