In redesigning a large number of my ships, I've decided that having larger ships generate enough power for FTL was too convenient and made balancing the factions varied FTL methods difficult (both for writing and game development.) To work around this, I'm moving the ships towards having large banks of capacitors/batteries that store energy for later use (FTL or other power-intensive equipment.) The ships would need to recharge off their reactors between jumps/warps.
This also presents a new weak point on many of these ships, I think.
Ships are powered by fusion reactors (plural for redundancy reasons) and store the excess power that isn't running the ship into capacitors and batteries for later use. These capacitors and batteries would likely work similar to those we have today but with advances in energy storage density. Fusion reactors have the added benefit of being the "safer" forms of nuclear power in that a runaway reaction is not possible as fuel is added on demand and to maintain the reaction. If a system fails and takes away conditions needed to maintain fusion, the reaction ceases. Contained heat and energy might disperse into the local hull, but the rest of the ship would likely survive.
Batteries would be used for taking over powering ship systems in the case of a local reactor failing while the nearest reactor transitions towards higher capacity of output to compensate.
Capacitors would be used for systems that require all of that energy in an instant: massive weapons with slow firing cycles and various FTL drives being the two primary examples.
Both of these capacitors and batteries would function much like what we have presently, only with advances in energy storage density. Batteries storing energy through chemical reactions and capacitors storing the electrons themselves.
If these ships were storing massive amounts of energy, astronomical by our standards since we are talking about faster than light travel, I could imagine damage to these banks causing a catastrophic discharge of the energy contained. Something that would likely vaporize the ship in a near instant along with anything nearby.
What would likely happen if they were struck in combat or something collided with the ship? And are there means to prevent this violent discharge, protect the ship itself from it, or redirect it away from the ship?
If it could be directed, I can imagine fleet formations being set up so that friendly vessels are never in the path of these discharges.