One idea I've been playing around with is less new tech and more old tech reengineered.
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Multiplex Warp Drives.
Essentially two (or rarely, more) smaller warp cores operating in concert with each other through a warp crossover matrix. Similar to the multiple cylinders of an internal combustion engine. There are several advantages to this setup.
• Reliability. Each core is operating at a lower frequency to achieve the same warp factor as a single, larger core. This puts less strain on each core and dilithium matrix, resulting in greater operational reliability, safer operation and longer service life. Further, each core can be shut down individually for maintenance and repairs without sacrificing warp capability, albeit at reduced speeds, facilitating more frequent maintenance opportunities.
• Safety. As mentioned above, the system is safer overall due to each core being operated at reduced loads, decreasing the risk of failures. In the even of a breach or overload, each core can be isolated and either shut down or ejected without sacrificing warp capability.
• Cleaner operation. Due to each core operating at a lower output, fewer waste products are produced. Further, due to the design of the crossover, overall emissions are significantly reduced, resulting in a smaller, more easily concealed warp signature. Lastly, the design causes less subspace shearing at high warp factors (the warp speed limit thing)
There are some disadvantages to multiplex warp drives. They are much more complex and require specialized training to maintain and repair, moreson than standard warp drives. They are much more difficult to build, requiring more time and resources. They also eat up more dilithium and antimatter, but not by a significant margin.
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Other things with which I've powdered my headcannon:
Isolated passive internal shielding to suppliment security forcefields. Small internal shield generators on independent power supplies covering sensitive areas (bridge, engineering, weapons, etc) to prevent boarding parties from directly beaming aboard in the event the main shielding fails. They activate automatically at yellow alert or higher and can be modulated to allow access by authorized personnel. Each one has enough power to operate for up to two hours after complete power failure.
Hybrid Transwarp drives. Essentially a blend of standard warp drive systems with Borg derived Transwarp technology. Safer and easier to build than quantum slipstream drives, though not as efficient. Utilizes multiple transwarp coils arranged into a nacelle configuration fed directly by warp plasma. Imperfect, causes a noticable wake and shockwave upon use. Cannot be used within a star system, not recommend for use within the galaxy proper, mostly used for inter galactic transit.