Personally I've never really had any problems with the whole swapping over thing. It would be quite interesting to see them all unified -- a complete revamp would probably be easier than trying to change each individual lane. Then we could make the lanes swap sides in Bretonia.
I have never ever had a problem with the cross over thing, I think I've run into an NPC doing that a grand total of once in all the time I've been on Freelancer, its honestly much less of an annoyance then when an NPC or player drops out of a lane right behind you or wants to enter at the same time you do and I don't see many people complaining about that.
Not to mention the fact that the auto pilot does the work for you, and it always knows which ring to go to.
(That and doing that would be an absolute bugger to code, unless I'm mistaken it would bugger up some NPCs and they'd have to be re-coded.)