the IDEAL Sins 2 environment-
Keep the gravity well system TO A POINT. What I mean is keep gravity wells, where they in essence are the control area of a planet; from planet menus is where you can build structures, and only in a planets (or MOONS!) GW can a structure be built.
However, Starbases, Mining Stations (I'll get to that), and some other things could be built by special deep-space constructors. Mining Stations would be used in orbit of stars or gas giants; mining helium for fuel, and nuclear smelting of metal/crystal. Also, mining plasma from a star's atmosphere could provide bonuses to energy capacities.
Stars project a HUGE gravity well around themselves. This gravity well is the area that allows anything that can be built in deep space to be built. At certain points on the OUTSKIRTS of a star system, would be a 'starlane' entry. Starlanes would be used as A method of system-system travel. An alternate method would be the construction of Jump Gates. These would be only usable if a ship has a 'Jump Drive' ability, and only for a faction's ships. It has the benefit of faster, but only two-way traffic. Starlanes, however, could have giant 'hubs', where several lanes overlap.
Now is where the DEEP deep space construction comes in. Whenever two or more starlanes overlap, they create a gravitational anamoly. Similar to a mini-star's gravity well, except there's nothing there, except for maybe some space junk or asteroids (nothing inhabitable anyway). Controlling one of these hubs would be very important.
However, there would also be research for super-powered jump drives, that don't require the use of a starlane (Starlanes would simply be the safest&fastest mapped routes); while a jump w/out a Starlane has a small chance to inflict damage to the ship jumping, it can be faster, and can easily be more direct.