OK, I have an idea for FTL travel which I think is simple, scalable, intuitive and doesn't require bringing in lots of additional complex rules and limitations.
Essentially, it's the existing "teleport" feature that's currently available as a console command, but accessed via an FTL docking block (or Beacon) and controlled with a menu which lets you make a "Hyperspace jump" from one Beacon to another. The construction challenge takes the form of requiring both Ship and Beacon to meet certain criteria before a jump can be made. Please consider the following:
Theory
Travel through normal space: Requires Engines to move. Engines require power. The total amount of power expended in getting from Point A to Point B is affected by the mass of the object and the distance travelled.
Travel through Hyperspace: Requires Engines and power in exactly the same way travel through normal space does, i.e. you still need a fixed amount of power to get from Point A to Point B. However, because distances and times are relativistically compressed in Hyperspace (insert technobabble), the power expenditure (and therefore the journey time) is instantaneous. The main problem is navigation as it relies on abstract mathematical calculations to plot courses between observable Beacons.
Blocks Required
Hyperspace Computer - Allows a Ship or Base to view the Hyperspace Menu.
Hyperspace Computer Expander - Reduces the warm-up time on Hyperspace jumps.
Hyperspace Motivator - Allows a Ship to make a Hyperspace jump. Requires a constant supply of Power per-second to remain active (like the Cloaker/Radar Jammer).
Hyperspace Motivator Expander - Reduces the cool-down time on Hyperspace jumps. Increases the amount of Power per-second the Motivator requires to remain active.
Hyperspace Beacon - Provides docking areas which ships can instantaneously jump to. Requires a constant supply of Power per-second to remain active.
Hyperspace Beacon Expander - Increases size of the docking area, allowing ships with larger volumes to use the Beacon. Increases the amount of Power per-second the Beacon requires to remain active.
Mechanics
Any ship fitted with both a Hyperspace Computer and a Hyperspace Motivator can make a jump. However, you are only able to jump to locations containing a Beacon. The Hyperspace Menu shows you a list of all the Beacons you can reach based on the total power stored in your ship. Locations which require more Power to get to than both the ship and Beacon have stored, or have docking areas too small for your Ship, are greyed-out or simply not visible at all. Each Beacon allows only 1 ship at a time to be docked at it. Beacons which already have a ship docked appear in red and cannot be jumped to until they become empty and turn "green". If you are already docked at a Hyperspace Beacon before you make your jump, then any Power stored in the structure the Beacon is attached to will *add* to the total Power available for your Jump. Upon completing a jump, you appear docked at the destination Beacon and un-dock in the same way you would from a regular Docking Block.
Both Beacons and Motivators are visible on the Hyperspace navigation menu. Beacons are visible permanently, but Motivators are only visible during their warm-up/cool-down times. This allows for a jumping ship to be tracked via your own Hyperspace Computer for a limited period, making stealthy jumps somewhat challenging.
Balance
Instantaneous power expenditure means that the more Power you have stored in your Power Tanks, the longer the distance you can cover in a single jump. Otherwise, you're limited to lots of smaller jumps with added re-charge time in-between. So, to have a fast FTL ship (one that can make the Kessel Run in less than 12 parsecs) you need to be more concerned about the total number of Power Tanks you have, rather than your Power output per second. The amount of Power required to travel a certain distance in Hyperspace could be equal to or higher than the amount required to travel the same distance in normal space. Adjust accordingly if balance is required.
Adding the power stored in Beacon stations to a jump allows ships to travel further than normal and naturally creates transport hubs. It also allows very small ships to make use of the Beacon network for more "domestic" purposes, such as cargo transport.
A Station designed to be a mass-transit hub would require lots of Beacons, Beacon Expanders and Power Tanks to allow Ships of different sizes to use it and keep traffic flowing evenly.
A Station designed to be used only as a Navigation point within less-explored space would require very few Beacons (maybe only 1) and enough Expanders to allow ships of whatever size you imagine will require use of the facility. You would only need sufficient Power Generators to keep it all active as Ships can use their own power for the Jumps.
Making the whole FTL system rely on total Power storage means a jump can be inhibited or disrupted entirely by hitting a ship with enough Powerdrain Beams. This would encourage Players to build "tackling" ships aimed at crippling other vessels instead of damaging them. Also, if a ship's shields are getting hit by weapons fire, it keeps firing it's own weapons, or is thrusting using it's normal engines then the time taken for it's Power Tanks to re-charge sufficiently for a jump is extended. This is a much more natural way of disrupting jumping than adding artificial damage limits, or creating specific "anti-FTL" weapons etc.
Expanded or Optional Ideas
Jumping to Planets: Planets create a large enough gravity well to be detectable in Hyperspace. As such, your Hyperspace Computer is able to plot a course to them. The upside is; you don't have to have already made a journey to a Planet via normal space in order to jump to it. The downside is; you will appear inside the gravity well of the Planet, so better make sure you have enough thrust to escape on arrival.
Emergency Jumps: A lot of people in this thread seem to be surprisingly keen on the possibility of being annihilated the instant you use your shiny new FTL system. To satisfy this death-wish, I suggest you have an option in the Hyperspace Menu for an "Emergency Jump". You still have to have a Beacon/Planet targeted, but this option reduces the warm-up time to zero and jumps you to a random location within the sector of the target. If your Ship re-appears in any space which is already occupied by another object (Asteroid, Planet, your own Base etc.), then any overlapping blocks on both your Ship and the object suffer immediate, extremely high area-of-effect damage which ignores shielding.
My Personal Rant
I hear a lot of talk on here saying FTL would have to be nerfed (long cool-down times, prohibitively huge energy expense to make a jump etc.) in order for it to be balanced. I fail to see the logic in this as everyone constructing an FTL system will have the same constraints, so it's naturally balanced. Ultimately, all we really want from an FTL system is reduced journey time. The main argument seems to be "people will use it to escape before I can blow them up". Well, so what? People will try to escape using any means necessary. Why should we bring-in rules preventing people from building a faster ship? It's a bit like accusing Han Solo of cheating because he owns the fastest ship in the Galaxy. So long as you can track your opponent then there's nothing stopping you from building an even faster ship than theirs if you want to give chase. Or just stop the other ship from jumping at all by hitting it with enough Powerdrain Beams. This game should be about presenting challenges which encourage creativity gameplay, not imposing artificial limits because a few players are complaining they came last in a race.
