Hands down one of the best mods I've seen for this game, and I've been around since Corvus was the only system...
But imo there are some ship variants that could be merged, changed or removed, here some examples:
1.The Balance Unto All and 2nd Null Flagship would make a good combination, merging both to create the Sylphon battleship would make a better encounter than fighting special variant 1 and 2.
2.The standard Rakia barely has any crew requirement/capacity, so a crew-less variant is superfluous. Either increase crew requirement or (imo a better approach) leave only the automated version, because AI phase cruisers are extra spooky and you wouldn't trust silly humans to crew an engineering jewel.
3.Automate the Valestry (ORN) version, or better yet automate all the ORN versions.
4.Give the Cieve an Apocatastasis (curious soul+scanner=obvious) and change its synergies to universals.
5.The Celika Ultra class increases its booster by 20% up to 100%, contrary to the description.
6.The Synastry EWAR cruiser is a good concept applied to a bad ship class. You want such a specialized ship to be fast and quick to exploit breaches, something the vast majority of cruisers aren't good at. My advice would be to get rid of that variant and make an EWAR destroyer of sorts.
Well those were my 2 cents, congrats on an awesome mod, looking forward to more of your work.