I didn't like the Frespace-combat as much, if I recall correct you're ship were allways supermanouverable, while the AI were usually flying in a straight direction, slower, with minor turns giving a illsuion of dogfighting.
Well, I liked the games as I do with most space-games, but I like it better the way it is in X now. The old X-games weren't any better back in the day, had basically the same solution on what I assume were bad AI. :-/
You can simulate the Freespace-combat feel pretty well tough, in some space-crafts, but theire not allways as easy to outfit, and dosn't suit all opponents, and one unique craft is very hard to get.
As for the 3D-thing, you're wrong.
The way the sectors are built up, is that they are basically a three dimensional cube.
And then there is a image wrapped around spherical ball on the outside of the cube.
This way all the systems get their own distant stars/planetary images and similar, and all the sectors (cube) vary in size.
So if you point your ship in one direction, and speed up time, and go away for a few hours, Your ship will come back on the other edge.of the cube, and start over again on the other edge, like in the old game called 'Snake', if you went out of the side, you came back on the other side.
It will never reach the distant stars on the image bent around the cube.
There is a few sectors where you can go to the planetary parts of the image pasted on the ball around the cube, and if you fly to long towards that your ship will be destroyed by atmosphere, on the planet.
But for the most part you need to use a Gate or a jumpdrive to leave the current sector (cube), or you wil come back to the start.
As for the Z-axis it is very usefull to be aware of when building space-station complexes with lots of complexes together, it is very hard to build a big station-complex very close to eachother without using the height axis.
Hit the insert key while on the sector-map, and the map will turn from X-Y axis, into Z axis, and hitting Inert-key again will turn the map back to the original X-Y axis.
It's alot easier to keep track of where you are in space, when you are able to orient height and depth direction.
Most of the objects usually gets generated within 50 km from the zero-line, on the Z-axis, so most of the big objects/stations aren't to hard to discover if you get the best radars, without having to orient too much in the heigth/depth of space.
This isn't allways the case tough, in the treasure hunt plotline, i've experienced to find some plot-items up randomly beeing generated allmost 100 km from the center on both sides of the Z-axis, and that is the range of three, and playership need to fly within scanner-range to discover it, kind of annoying in a big system like Akeela's Beacon..
Alot of people want planetary landings and similar in the next game, but I don't.
The big rock in Aldrin is bad enough..