I don't know if there is still discussions about that, but I thought of something. I personaly love the phase-lane method. My idea is to be able to discover new phase-lane as the game goes.
Having a civic research (high-level) adding a "phase-lane navcomputer" to the scout frigate would enable the frigate to explore around and try discover new lanes. Of course, discovering new lanes would take time, so the frigate would have to move along the edge of a gravity-well, slowly and at some places (in fact the lane exists, but they are invisible and unusable until discovered), the frigate would find one.
Oh and I know that this might sound "no need", but personaly, I would like a visual explanation on why does planet x don't have a phase lane with planet y even if there is nothing between them. Having an asteroid belt or a space cloud of something would be a nice visual effect in my opinion. I'm not talking about the gravity wells being asteroid fields, but a real asteroid belt on the map.
That's about it!
Thanks for reading.