I remember suggesting that you play it the other way and avoid other ships as you fly though "if you have to have a mini game mechanic". I haven't played since but I believe that it was changed to be something of that nature.
I, unlike many, like the idea of highways. I think it's an organic way to streamline travel within "sector style" X Universe. It makes sense to zip through sectors on a fast lane vs the time manipulation system in other X games.
Implementation is key. I think the way to please everyone is let these highways be highways. Lets call them acceleration void tubes

Another cool part is let me jump out of it maintaining my speed. What I mean is, you are going at 1000 and jump from the top. Your ship doesn't magically and instantly reduce speed to 500, but either slowly decreases at a normal rate to 500 or keeps that speed, say if you are using Newtonian flight system without assists. I can see very fun and strategic game play scenarios where you can sling your self our of a tube to reach a far off station, or get into a fight quicker, or through a hostile environment etc.
tldr; Highways should be treated as speed multipliers. Highways multiply your possible speed but don't limit your control in the them or the speed that you fly at. You can additionally sling out of them without loosing speed and shoot at ships while in a highway.