I think that FTL should be both ship-based and beacon-based.
In order to use a beacon, a ship would need an on-board system, the size of which would determine the amount of power that the FTL system could hold, and power fill rate. Larger ships would require more power to warp.
Beacons are just waypoints and energy input for the station FTL system.
Each FTL system block holds 50,000 e, and both the beacon (station computer) and FTL computer (ship computer) hold 200,000 e
There would be three types of jump:
1- Safe jumps
-Beacon to beacon
-Ship cost: About 1,000e/1 mass
-Completely safe
-Station cost: 1,000e/1 meter for both stations
-If the ship or station runs out of energy, the jump does not occur, and no energy is drained.
2- Emergency jumps
-??? to ???
-Selects a random location within your possible jump sphere (margin of error of 50%)
-If you warp into a collision, it just deletes the part of the ship inside the collision. (if the core is deleted and the player is inside, the player is killed)
-Ship cost: About 5k/1 mass + additional penalty for ship size + penalty for distance jumped
-If your onboard FTL system can't hold enough power for the jump, it starts pulling from your normal power storage, when that runs out, bad things happen.
3- Warp jumps
-A safe jump, from space to a node, using your ship as a node
-Your ship shoulders the energy price of both the ship, and the sending beacon.
-If the node you're teleporting to is gone, preform an emergency warp instead
-The destination node is hardwired in an expensive block, to set a warp to the block, activate it while in range of the node.
Edit 1:
-Stations use energy based on the size of the bounding box of the ship they're transporting. Eg. a 100 by 120 by 350 ship would require 4,200,000 e for both stations, on top of the distance cost.
Edit 2: Clearing up some things:
-Beacons a just beacons. All the limitations lie in the FTL system on the ship and station.
-The FTL system blocks can be connected to a beacon to be a station FTL system, of a FTL computer to be a ship's FTL system. Station FTL systems would recharge over time, while ship FTL systems would only charge when warping. (They charge so fast that there's no power left in the system - no shields recharge, no weapons, no turrets, no movement.)
-For an emergency jump, a station must allow the connection. Connection settings can be set per faction, distance and player.
Edit 3:
-rece ktore lecoz mentioned something in a post I thought was a good idea: ships loose all shields and 50% remaining stored power when jumping. You would not only need a good power supply, but a good defense system for an FTL gate.
Edit 4:
-Rebalanced energy costs slightly on the ship's end, to make Emergency jumps possible, and normal jumps less expensive.
Edit 5: Some math:
Standard jump with a 50m wide, 75m tall, 125m long cargo ship:
For the stations:
Distance cost: 16 sectors (star system width) = 16 sectors*1,000 m / sector (sector width)*1,000 e /m = 16,000,000 e or 16M e
Ship dimensions cost: 468,750 e
Total FTL jump cost: 16,468,750 e for both stations.
For the ship:
1,000 e/ mass * 0.1 mass/block (most ship blocks) * (468750/2 blocks, estimate) = 23,437,500
Average ship generation for a ship that size: 500K-1M e/s = 24s-47s charge up time.