So I just read the entire thread. I have an idea, so bear with me.
Suggestion: Add a "spark recalibration time". For each 1000m*some_multiplier you teleport from or to gamma or beta, you add 1 minute to your spark recalibration timer.
Your spark recalibration timer will accumulate from jumps up to 24 hours ago in which time after it will start to clear. This will make people think about where they spark to and prevent excess abuse of fast travel. Jumping back and forth to a far away station would add quite a bit of extra calibration time, you would need to pick and choose sparks wisely else you could wind up with a timer that lasted quite a while, but obviously never more than 6 hours or so.
By doing this you would have to choose your sparks wisely and you couldn't use it to jump around rapidly too much. This would give back tactical relevance to where your staging island is. Now granted there would still be easy ways to game the system such as jumping around multiple alt scout characters but technically you can already do that anyway without spark teleport so it doesn't matter too much.
Dev Zoom, I know you remember why intrusion 2.0 was put in place. It obviously was for a lesser reason than what the current spark teleport system enables. We shouldn't be encouraging spam of fast travel mechanics unless there are serious drawbacks to them.
An easier solution is lowering the spark limit to 5 locations, that would at least limit the scope of power projection the current system enables. Still though the fact that its instant and without a cool down still opens this solution to abuse even with a more limited scope.
EDIT:
I don't see alliances using spark teleport for sap defences as a problem. Showing up to defend your outpost is important. Too many defenses in one day will obviously wear any entity under attack out. What I do see as a problem is abusing sparks in combination with detectors and then projecting a force to an island every time its used. Spark teleport is a good feature for convenience and pinpointed strategic uses. We do need to stop any potential for abuse via excessive power projection in combination with scouting as well as giving staging islands locations tactical significance. If you want to fully control your islands use you really need to be there.