So, I thought I'd toss out a few things that I've noticed. Part is going to mirror some of the OP comments above (with caveats), but I'm also noticing that a lot of the other ships are pretty severely underpowered.
Yes, some of the bigger ships are OP, which is to say 'Elite-tier'. You might consider a split like many other mods where they have a Special Division that has better ships, and then the Civilian versions.
Most of the other Med, and especially Small ships seem to lack flux dissipation and capacity. While I haven't crunched the numbers, I keep comparing these ships to other more established Modded fleets (Imperium, Apex, Dissault, Diable, to name a few) and sadly, I keep passing them up over and over again. That doesn't mean they suck, it just means that in that class there seems to ALWAYS be several ships that shine more.
SO! ^__^ I have a suggestion!
Make really good merchant ships.
Just gonna spitball a few ideas out here -
Is there a way to make rearward-facing shields? 'Cause a merchant ship that can keep its speed and have rearward facing guns/shields would be powerful AND generally useless at offense.
Is there a way to make, create, forge, or otherwise increase the staying power of fleets abroad? I've seen a few crude mods, and LOTS of flavor text talking about it, but little in the way of actual gameplay.
Consider some S-Mods if necessary
Split your Civilian versions (most of which are just fine) and consider a full faction? The Merchant Marine, Gray Market, or otherwise semi-professional army doesn't feel like it's been done, or done very well. Dockworkers Union, or whatever. Sturdy tankers, fast speeds, purely defensive for the Civ aspect, and (almost) purely protective for the Military half.
A lot of this you've already done! Which is awesome. But it feels like a partially-implemented idea.
I hope you'll keep working on it, and evolving the concept.
Find a niche, and expand into it!
