remove the 1000Ly limit (why was it even limited like that?)
Because the farther you want to go, the more possible paths there are between you and your destination—exponentially more—and therefore, the more time and processing power it takes to find the fastest or most economical route you desire. (The devs
have stated that the planner uses a modified
A* search algorithm.)
If you go closer to the core, you'll see that the route planning limit drops drastically, owing to the greater density of stars making the algorithm chug even harder.
So while the 1000ly limit is not a "hard" limit—it could theoretically increase if the devs could optimize parts of the algorithm or the underlying graph of the galaxy—it's actually pretty cool that they managed to bring up that far. As mentioned, it covers pretty much anywhere you want to go in the Bubble.
I agree with your other points, though. More options to affect the route planner, or to customize a planned route, would be awesome.