I haven't been playing Cosmoteer but here are the most Neo-Z ship designs I love and proud:

Protostar Guardian
Upgraded version of Protostar Decimator. Vaporize a single target but unstoppable and can take a single large ship in numbers.

Protostar Mega Vanguard
The latest design of my Protostar Arsenal. Has more shield than The Guardian. It damages the shield, cuts the ship into pieces then vaporize them.
The most remarkable mods I use are Stargate and MicroTech mod. Seriously, Micro shield is extremely damn overpowered that Ancient Armies use it.
Mega Vanguard has Pulse Beam from NWADM and Minigun mod.
You can actually make overpowered ships only using MicroTech and NWADM. If you also use KodenameKannons armor, you probably don't want to roleplay with them because they are way too godly unless you are struggling like Azura (Azura's Wrath reference).
Also, despite their protostar name and strength, every ship's weakness is fire. If you want to counter them, just burn them. The subsystems will be unoperated and you can attack the them very easily. Use flamethrower from NWADM mod.