The idea of hidden lanes sounds particularly interesting, how do you envision that?
So here is how I think it would work:
a) You give all your scouts or diplomatic vessels (better if it was a science vessel) a new researcheable ability called "survey system".
b ) A little like exploring a planet you explore the gravity well and perhaps a little beyond the gravity circle.
c) There is a chance that this research will turn up an unexplored phase lane.
d) The scout frigate must enter the phase lane and explore the lane. If successful the lane would be marked but kept secret because it would be unstable or not mapped properly for 100yrs of experience using it that that takes.
e) Only ships with level 10 experiece (you need a good navigator) would be able to navigate the wormhole with a limited number of ships per jump. These ships would potentially come out damaged on the other side. Alternatively perhaps secret phase lane navigation could be a researcheable tech tree item. Once researched spies would tell the enemy like they do for a novalith that somebody has found a secret phase lane prompting others to explore as well.
f) The unstable phase lane could be collapsed with the correct ships/tech by the player. Alternately different tech could strengthen the new phase lane
g) The discovered phase lane could lead to a new planet or the enemies rear or something else like a new alien species or a minor faction. Primarily though you would want it to cross phase lanes somewhere across known space as some sort of alternate route.
h) The enemy can see ships arriving or leaving at either end and will then know to explore that gravity well...... which would lead them into your rear. Now if the player does not notice your ships arrive with a bright "entry effect" from the non standard phase lane. Then it should just look like your ships jumped there normally and were not noticed...
P.S. Perhaps phase lanes collapsing or becoming unstable could be added to the game to go with the spinning.