I see two possible changes that could be made to the phase jump system that would remove some of the "choke point defense" strategy a lot of people have been concerned with. I've been thinking about these for a couple day, and waffle back and forth on which one I like better.
Both assume the game's been changed so that you can't jump through the gravity well. I've been seeing some posts from the devs that they're looking into how to implement that. My idea would be that:
(a) Phase jumps are straight-line movement
(

You can't travel through phase space inside the gravity well.
This leads to a mechanism where you'll get opposing hemispheres of "jump from" and "jump to" between systems. You can't always reach every "jump to" point from every "jump from" point. In fact, the only place that works is what we now think of as the jump lane.
So idea one is that the "jump lane" is a symbolic marker that you have the range to jump between those systems (and the shortest jump distance between those systems). As range increases through research, new "jump lanes" are added to the map. Each faction would have a different set of lanes, since they could have different research levels and/or faction abilities that would increase range.
If you just click the move between systems order, it'll default to shortest time (which would be the current lane). If you hold the mouse click and drag left or right, you'd move the emergence point clockwise or counter-clockwise around the gravity well semicircle you could jump to. For a multi-system move, you'd optimize fleet travel for shortest time until that final jump where you'd hit the location you specified.
The time it takes to travel in phase space would probably have to increase some to make the jump lane strategically important. However, if you're invading a system, you could take the time penalty and emerge along the system rim where the opponent hasn't placed fixed defenses.
Idea two ties the jump lane to a pair of gate structures. Small ships (frigate class and trade vessels) must use the gates. They're too small to mount full-up jump drives and weapons and everything else. Capital ships can jump without gates, using the same mechanism as idea one. As you research range increases, you can build your own gates to link previously unconnected systems (if you own both systems).
This makes the frigate-class vessels exploration and system defense vessels. The heavier frigates could be used in an attack of a lightly defended gate. Heavy fixed defenses would require a capital ship fleet (they could come in out of range and flank the fixed defenses). If a system has heavy fixed defenses, a large mobile fleet, and there's no other path around it, you should be stuck.
Idea two also gives some uniqueness to the cruiser versus heavy frigate. They might have similar combat power, but the cruiser can be used in independent raids, like the cruiser class was intended to do.