I like your idea of dedicated lanes in stations. I have this sort of already on some planets where there is a traffic grid. I am going to leave some planets and stations this busy because I want it to be like you're in an annoying traffic jam sometimes. I don't think it takes too much time. I've been in them many times myself, it just takes a bit of concentration to navigate them.
I don't know why you got a fine for 50k from security. It sounds like you ignored traffic-control. When you enter a star-system keep an eye on your bulletin board. An orange message might appear there that you can click on. You will then be asked to state your destination planet. Ignoring this message is taken very seriously by most factions. The fines will normally appear in your item panel and you can hover your mouse over them to see what they are. However ignoring traffic-control is like flying a plane into US airspace without clearance and without identifying yourself. Maybe 50k fin is excessive but in the beginning even if the fine is 10k many players won't be able to pay it.
As I'm thinking I might make the traffic-control message blink continuously to alert players more to the fact that this needs their attention.