Changes to Drives
Capacitors
These are essentially incredibly powerful batteries that store energy in superconducting loops, super charging your energy weapons or other devices with burst of power. They give [Energy+Materials] effective surplus power but have several limitations on use; only only system per ship can be sustained, and they need to be topped up from a much larger power source than a ships engine core, and thus only function in orbit of worlds you control with factories and shipyards (a Twist Drive ship could use its capacitors to jump away from such a system, but not back).
UV Laser
These laser cavities produce a much shorter wavelength of light, and thus when pumped have much more stopping power than the longer wavelength lasers that need to ablate off surfaces rather than drill a hole. They thus have the same base damage but gain +2 from surplus power rather than plus 1 and are slightly more expensive.
Advanced Radiators
Currently a ship can only have surplus power ratings less than or equal to its ship size before it melts itself with the heat of its own engines and weapons. Advanced radiator elements built with superconductors and other tricks are far superior to the basic ones that are implicit with building a space ship, and raise the surplus power ceiling by 3 with each unit, in addition to the 1 they provide from increasing ship size.
Pulse Drive
With a better understanding of the mechanics of gas flow, a simple fission rocket can be given a reaction chamber that can vary its geometry - this vastly improves specific impulse to a level equal with fusion drives as well as allowing unprecedented control over the propellent stream to aid in fast manoeuvring. These dynamic systems do come with an energy cost however. IP drive with speed 2, gives +2 dodge and costs -1 power. Useful for small ships that need to close fast with the enemy like laser gunships and assault craft.
Intrusion Unit
With a combination of grapples chaff, and quick launching penetration pods an intrusion unit can insert troops and EM measures into enemy ships and space habitats when at ramming range, allowing the aggressor to take control. The act of forcible entry damages the victim severely, and nearly all vessels have command locks, thus stealing ships outright is vanishingly rare, but they do disable opposing military vessels and pillage the contents of cargo vessels and station stocks.
Light Sail
A suitably light and reflective material can bank and ride about a system on the photon winds of the star itself, lugging along a payload beneath its vast mirror sheets and hundred kilometre rigging. Whilst it makes the vessel pathetically vulnerable and unmanuveourable the sheets are extremely cheap once sufficient knowledge of weaving molecules has been gained, and since the thrust is effectively free a sail can lug along a surprising amount of cargo in its minimalistic frames (halves the cost of cargo bays, cheapest IP drive).
Lithium Sinks
One method of heat management on a spaceship is to use excess heat to melt down a block of material in a heat sink, thus allowing longer and heavier energy usage in combat situations before the sink fluid is vented or refrozen. Whilst basic sinks on the current spaceships use ice or mercury, the element lithium has the longest window between its melting and boiling point of any material (that isn't radioactive or really expensive) whose melting point starts at a reasonable range and thus can be used as an efficient and flexible heat sink on a high energy warship (Tin also has similar heat capacity but sounds less science-fictiony ) storing heat up to a thousand or more degrees Celsius. Addition of a lithium sink will boost the energy ceiling of a ship by 10 units, but only one can be installed per vessel.
Interceptors
Specially designed high thrust missiles that act almost like tiny spacecraft, the Interceptors attempt to destroy a foes missiles whilst they are still closing using kinetics and ECM. If they roll to hit successfully they destroy the opponents missile salvo (or if there are no opposing missiles, do some meagre damage), providing protection to a whole friendly fleet.
Pebble Defence
Small linear accelerators with automatic targeting can do considerable damage to even the most formidable of incoming missiles, and their drive ability can even move the ship to dodge a beam or bullet. They do require both considerable energy and computational support however. +1 dodge per Computational Module, requires 1 power.
Needlegun
Rather than the solid slugs of a Railgun, the needle gun takes its matter from a reservoir of molten metal that is accelerated, shaped, and heat all within the length of the gun chamber. It thus has both higher base damage and can be tuned to drill though various designs of armour with a rapid patter of pulses. They thus ignore the first two points of armour.
Viral Bombs
The crudest sort of wet biotech is that designed to kill, and the specially build delivery shards of this weapon system contains a veritable host of active deadly species and designs. Unlike most bombs these can only damage population, not facilities. Each successful attack has a 25% chance of adding the poisonous trait to a world with an atmosphere, and a 25% chance of dealing damage again the following year if applied to a world with a biosphere. Does considerably more damage to target populations with low genetic diversity.
Heavy Cladding
A design rather than technological improvement, Heavy Cladding refers to the practice of bulking up a warship with rock and slag to absorb the pummelling of its foes energy weapons. Any sensible peacetime designer would abhor the wasted volume and extra mass, but the needs of war sometimes make the option practical. Only one unit can be installed per vessel, and it massively increases the armour rating at the cost of the ships IP speed and dodge rating. It is thus advisable for large ships facing beamers of medium size and above, increasing toughness at the cost of sacrificing their remaining dodge and power verses missiles and agile foes.
Composite Armour
By using layers of ultrahard ceramics and layers of non-resilient soft extremely impressive armour can be created. However good materials and positioning knowledge is required before using composite defence is superior to just cladding additional titanium around a ship.