The specifics of inter-system travel are TBD right now - we'll likely end up trying a few things before settling on something that feels right.
I will say that I prefer the Star Control 2 model where you can go anywhere to the one with fixed lanes between the stars. Functionally, I suppose they're very similar, and the one with lanes is a reasonable simplification - but for me, it detracts from the feeling of free exploration. There's that feeling of actually being in deep space, which I find very immersing - and the "lane" systems I've seen gloss over it completely. Not to say that it couldn't be done, though.
I tend to agree that Free Exploration is great, sometimes it seems that wormholes or warp gates or lanes reduce the vastness and openness of space, and simulate, in a way, planetary terrain like mountains and rivers, etc, as natural barriers. However, like Thana mentioned, the points of focus and defense they offer have some usefulness as well, specifically if you are trying to insert story or a tiered difficulty of content, tough choice for sure.
Maybe a compromise is possible, if you have various lanes and such, but then have the 'Option' of paying a premium of 'Credits/Dollars' (or whatever the monetary system will be in Starfarer) to access systems off the grid that you would not normally currently have access to via lanes/gates. This would allow some freedom, and provide the possibility of surprise type attacks from beyond the 'front lines' of the lane/grid/gate system, while still keeping a certain linear progression in place for the most part.