How about... this:
The Gate system isn't a point A to point B thing, its a web, with multiple paths intersecting one another. The gaps in the lanes allow for entries into the web for anything that happens to be there. It seems less that its purely a technological limitation and more that its also a design feature to allow for ease of access. At the same time though we know that gates can be reprogrammed to have a different destination, so the gates being "paired" can't be a permanent thing.
OH. OH. ALSO.
Planets move and stuff, so point A to B setups are going to be disrupted anyway by gravity wells and other annoying things at different intervals. BUT. If the web was for the most part ABOVE the solar plane (I.E. above the planets if we use the relative orbits of the planets as a plane) then the web might actually be far more extensive than we get to see, with gates anchored next to planets, then gates above that to "enter" into the web, and then artificially anchored gates in-between the planets themselves spaced in such a way as to overcome the orbits of the planets themselves. Because of this, gate pairing would need to be dynamic as the system is constantly changing. This would also suggest that interplanetary transit has seasons in which going from one planet to another might still cost more because you gotta jump more times cause its like, all the way fricken over there now instead of where it was 6 months ago.
Since they're spaced the way they are, this would allow the gates to be produced cheaper and more plentifully, making the saturation of the system in gates far more practical.