Hello. A long time lurker and the idea of Newtonian Aurora makes me as excited as the prospect of a lifetime supply of chocolate.
The lack of jump gates did make me wonder how you were going to handle orbital constructs (Fuel harvester stations, orbital habitats, shipyards, e. t. c. ) as they would have been limited to where they were constructed, which sort of defeats the point.
But instead of allowing the space station being able to move and then jump themselves, why not have a construction module that only allows construction of 'space station' designs?
Maybe allow construction facilities to still build space station designs so you can still easily build them in highly developed systems, but for newly aquired systems allow two options;
Pre-fab space station constructed at a developed colony, transported to the new system in freighters and then constructed by a construction vessel. (Much like engineers could do with PDC's but faster. )
Construction vessel builds Space Station on site - Would require the construction vessel access to resources.
The only problem I can think of with both of the above would require access to pre-fab parts/resources and therefore wouldn't be able to be built around a non-habitable planet and would have to be tugged into orbit of these planets. Though that wouldn't work in systems with no planet you can set up a temporary colony on. Unless ships can draw resources from other ships in the fleet, instead of from a colony? Which I don't think is the case as the current gate construction vessels don't use any resources at all.
This would mean that you also wouldn't be able to have a heavily armoured space station jumping a fleet of non-FTL craft into an enemy system, so would be able to allow heavily armoured/armed defensive stations too, possibly? (With a huge maintenance bill. )
As for expansion of shipyards, why not disallow expanding already built shipyards? I'm not be an engineer, but I can't imagine the frame and infrastructure required for the construction of a 5k ton vessel ever being able to be increased in size to support the construction of a vessel that is 10k tons without taking everything apart and then re-building the facility. If you allow the construction of shipyards at set sizes, it means that shipyards will not have to grow from the 1k ton sizes they currently start at. So, if you're building 10k ton ships and then get the urge to build a 50k ton military behemoth, instead of increasing the size by 10k each time, you'd design and build a 50k ton shipyard.
It would also give the player a chance to plan out. Do you build a 5k ton shipyard to start churning ships out immediately and then build a 10k ton shipyard at a later date for larger vessels, or put a bit more time into the shipyard straight off and allow you a bit more flexibility and the space to grow your ship designs.
Of course, this is just an idea and might be in a completely different direction to what you want to do.
I tend to have lots. (With most being completely whacky. )