Use real physics for interplanetary flights - computing orbits, acceleration/deceleration burns, landing on planets and taking off, docking with mothership or space station. All can be done using autopilot or manual controls.
Using telescopes, radars, spectrometers, etc. to obtain data about stars and planets from distance. Mapping a planet's surface by orbital survey: landscape model, mineral distribution, atmosphere composition and properties. Launching automatic probes to quickly mp all planets in the system. Deploying landing probes, taking ground/water/air samples. Driving remote controlled rovers. Landing on a planet in an aerospace shuttle, flying under the ocean surface with aircraft-like controls, walking in a space-suit, driving in a rover, and using ground buildings.
Collecting hydrogen from gas giant upper atmosphere for ship's engines with magnetic ram-scoop. Collecting minerals from asteroids/planets with harvester ships and transporting them to building sites.
Constructing modules for the mothership or an entire ship on orbit using minerals from harvesters and nanoassemblers (nano-robots) or "3D printer". Constructing/upgrading mothership with dockable modules. Constructing utility ships or small modules in onboard nano factories. Constructing ground buildings with nanoassemblers using local materials. Self-repairing of constructions using smart nanomaterials or nanorobots. Manual repairing in some difficult cases.
Building bases, domes, cities on planets or building space stations. Building passenger ships and transporting NPC citizens to new colonies. Building orbital fuel stations, a fleet of harvesters, orbital factories, etc. Probably: terraforming.
Importing new models and scripts, with moderation on the main site. Development of scripts for autopilot, defense systems, and warships. In-game exchange and trading of created content between players.
Exploring, harvesting, building, colonization in cooperation. Help with repair and evacuation. Server database will save the name of the pioneer of a system/planet and names that he/she gives to them. Trading with ships, colonies, resources, new models and scripts, and programs. Player-vs-player fights in space or on a planet using realistic physics (very hard and expensive).
The player starting with a big starship with a certain degree of autonomy. The ship can make interstellar flights to nearby stars (or rather, to the stars whose relative speed is not greater than 50 km/s - more on that below), carries a bunch of probes and 1-2 shuttles to land on the planets, and has a small onboard plant for the production of equipment and modules. During the game, the ship can be upgraded, but up to a certain limit. When a player accumulates enough money, he can buy a better ship, with a greater degree of autonomy and "range" of flight. Some ships have a modular design, i.e. theoretically can be completely reconstructed, some do not allow upgrading (e.g., atmospheric shuttles). A player can have a lot of ships and manage them remotely from the ship or station, where he is today (like in strategy games). Communications are instant regardless of distance.
The center line of the gameplay is research. The ship is equipped with multiple scientific instruments - telescopes, radars, spectrometers, descend probes, etc. To explore the planet, you have to launch several probes into its orbit, and wait a few days of real time while probes will make a lot of turns around the planet and will map the entire surface of it. The longer probed the planet, the more detailed information you will get (eg, elevation map and distribution of minerals). To get detailed information about the surface conditions - temperature, pressure, etc., you must launch several landers, including remotely controlled rovers, or land yourself using the shuttle (if the environment is not too extreme). Probes can be destroyed by high pressure and temperature, acid clouds, etc. The accuracy of the data depends on the equipment available to the probe. It is possible to take samples, including biological, and bring them to the main ship's onboard laboratory for more detailed investigation, or move to the other players or to a planet with NPC scientists.
The main worth are unusual and new discoveries - the planet with extreme conditions, planet with life, planet suitable for colonization, double black holes, etc. The player can give names to stars, planets, geographic features he have discovered, and type descriptions for them. This information is stored on the server and displayed to other players when they come into the system. Through the server, you can search the planets and other objects by any set of parameters, i.e. the ranges of size, weight, distance to the star, etc, like in the Star browser in the current SE version. But in the game, the search will perform only in a database of objects which was studied by players. The player may decide not to add his discovery to the open database system, ie make his discovery private, but then the rights to name the planets will be given to another player if he accidentally discover this system independently.
In addition to research abilities, the ship will have ability to manufacture various stuff using 3D printing and nanoassembly. In particular, good plants can produce the parts of a new plants or a new ship, which then can be assembled by robots. A bunch of various resources are necessary for production - different chemical elements that can be extracted from asteroids, comets and planets using bots or harvesters. The plant can also be built on the planet. In addition to the plant, it is possible to construct various buildings, ranging from the climate station and ending with a full-fledged colony or city. Construction time depends on the amount of work and on the speed of delivery of the resources. For example, a small probe can be made on the ship within 10 minutes, but a colony on the planet is built for many months or years (of real time). Stopping of delivering of some resource suspend the construction.
Colonies are populated by NPC people and can bring certain benefits to the player. For example, cheap or very fast refueling, repair and construction; set crew for expeditions (affects the speed and quality of operation in laboratories and factories). Transportation NPC's to populate the colony from another planet on a passenger ship (including automatic ones) also makes a profit. The quantity and quality of suitable NPC crew members depends on the population of the colony. In dependence on natural conditions and level of development of the civilization on the planet, it may have a small base with two robots or a thousands of cities with a 10 billion population. The most populated planets in the beginning of the game are the Earth and 10-20 its first stellar colonies.
Physics of the spaceflight is the realistic as possible: Newtonian mechanics, gravity, aerodynamics. Main engines are jet, antigravity will not be used in SE universe. The realistic physics yields to the concepts of the specific impulse, the propellant expense rate, orbital maneurs, etc. Therefore, the complexity of any research or resource extraction will be determined by the delta-V quantity - the total changing of the ship's the speed needed to complete the mission. For example, to exit from the Earth's low orbit to the interplanetary flight, you need 3 km/s of the delta-V. For take-off from the surface of Mars to its orbit you need 3.5 km/s (orbital speed) and additional 2 km/s to lift up and exit the atmosphere. To harvest ammonia from that comet, you need 18 km/s and 6 months of time, but to harvest ammonia from this icy moon, you need 45 km/s and just 2 days - the choice is yours. Nearby stars are moving at a speed of 20-30 km/s relative to each other, but there are stars as fast as 100 km/s in solar vicinity. Stars on the other side of the galaxy in general are moving at a speed of 500 km/s relative to the Sun. The hyperdrive allows the fast (several minutes long) flights between stars, but it will save the physical speed of the ship. Therefore, if the maximum delta-V of the ship is just 50 km/s, these fast or distant stars can not be reached (more precisely, you will have not enough fuel to brake your ship near their planets without using air-braking). The amount delta-V is determined by the fuel tanks volume, by the specific impulse of the engines, and by the vehicle's weight (so thin framework constructions are more benefit than heavy shielded hull).
Controls over the ship can vary from hardcore fully manual (in reality it is almost impossible and very risky to control the spacecraft manually) to fully automatic - the player simply selects the target, ask the computer to calculatу the most evvective or most fast course, and launches the autopilot. It also will be an "intermediate" solution - semi-automatic mode, where player will make some actions manually, but with prompt from the computer (like in Orbiter). In some cases, manual control is more convenient (for example, an overview flight over the terrain in the shuttle). During the long automatic flight, player can switch to control another ship factory, colony, take analysis over the data collected by the probes, communicate with another players, etc.
In addition to resources for construction, you need a working body (propellant) for ship's engines. Normally this is a hydrogen, which may be produced or collected in different ways. The easiest way is purchase it at a orbital fuel station near Earth or any advanced colony. But rather good ships can collect it themselves - extract hydrogen from ice of a comets or icy moons using harvesters, or collect from atmospheres of a gas giants with a magnetic air intake. Different methods and different models of the ships could do it at different speed and efficiency. The fastest way is to replace an empty propellant tank with a full one at a fuel station (5 minutes), the longest way is to collect hydrogen from atmosphere of a gas giant (many days). At some point, the player could build their own fuel station with a fleet of automatic harvesters running between the station and gas giant or icy moon, and take profit from other players by allow them to refuel on his station. But in the long expeditions in an unexplored system, you have to carefully monitor the propellant expense rate, to prevent finding yourself with empty tanks without the possibility to return to the civilization.
In such case, you can switch to another ship and bring it to the one which is stuck without fuel, and refuel it. Or you can call the other player to help you. The ship can be damaged or even destroyed, if you pilot it careless. Ship can perform minor repairs by itself, but serious damage may require the assistance of other ships or players (for example, if the ship can not move due to destruction of the engines). If the player's character was in the ship when it was destroyed (for example, by an unsuccessful landing or docking) he dies, and his property (ships, stations, bases) goes "inheritance." This mean what player can create a new character with new name, which will inherit the property of the died one. Also, ships and space station, bases and colonies on the planets can be damaged and destroyed by natural disasters, such as meteor shower or volcano eruption.