I posted an idea to mitigate this a while ago. After a search, I finally found it (it's slightly modified from the original to better explain the idea):
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I can't say this is my idea because I first read something along these lines elsewhere on the forum (can't find the post though), but how about this:
Pressing 'exit FSD' brings up a set of targetting squares on your HUD which your ship automatically flies through while your ship's computer calculates the complex maths needed to reinsert you back into normal space.
The course of the squares would take you looping around your destination (or spiralling in the case of asteroid belts), gradually taking you closer and closer, whilst 'under the hood', the server is finding an instance to drop you into (or creating a new one).
IMO, the good thing about this is that the time taken doesn't have to be fixed, and you're essentially helping the server place you in the correct position to emerge in the instance where it wants you to be.
You do retain a certain level of control of the ship during this process, and deliberately deviating from the path through the squares would mean that your ship's computer needs to start the calculation over, so it would be expected that deliberately steering out of the squares would make the calculation take longer (or lead to the attempt to reinsert into normal space being aborted).
Keeping bang in the centre of the squares as you pass through them would result in final emergence close to the destination (space station etc), whereas keeping totally hands-off would make you emerge further away (say 20-30 Km). The ship self-steers to some extent during this process, tending to drift towards the edge of the squares.
It would like a fiction-compliant mini-game, but a relatively easy one to play (I know 'mini-game' is an unpopular term, but this one would seamlessly intergrate and wouldn't feel like a mini-game, and IMO it's much better then the jarring effect we have at present).
Traders worried about being attacked outside the no-fire zone would want to emerge as close as possible, so have a vested-interest in keeping as close as possible to the centre of the 'navigation' squares. Others who don't care could take this opportunity to remove their hands from the controls and have a sip of tea/coffee/beer etc.
I can't find any videos to illustrate the sort of thing I mean, but the closest I can think of is that scene in Aliens 2 where the Marines are going down to the surface in the dropship, and the pilot says '5-by-5 we're in the pipe'.
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