Endless Space 2 is seemingly just a typical 4X game, however, it contains an incredibly high level of detail and the player can quickly become lost among the countless options and sources of different benefits to the empire. While starting each game you should definitely keep several things in mind, especially if this is your first encounter with this game.
1. Select the human faction (United Empire) for your first playthrough. This way, it will be much easier to manage your empire. They employ classic solutions, their ships have the ability to mount larger numbers of modules, and they use Influence (one of the basic resources in the game) for the purposes of speeding up production, research, etc. They can also colonise a greater amount of systems before reaching the approval penalty, which is connected to having too many systems under your control. Alternatively, you could pick the Sophons (bonuses to exploration and science) or the Horatio (greater population of systems, upgrades to your population but more expensive vessels).
2. In the game you will often encounter the concept of FIDSI. This is an abbreviation for the five basic resources in the game: Food, Industry, Dust, Science, Influence. Food, Science and Industry speak for themselves, but Dust is the primary currency when it comes to buying resources or accelerating production. On the other hand, Influence is used to expand the borders of your empire and is also used during negotiations and diplomatic talks.
3. Systems are the basic territorial unit (the equivalent of cities in Civilization, provinces in Europa Universalis or planets in Sterallis), and not the planets in the systems. However, the more planets in the system, the better. Such a system will accommodate more population, will provide better FIDSI income (basic resources) and will have better chances of anomalies or strategic and luxury resources. Each planet has a different set of bonuses to the relevant FIDSI branch and to the approval. In the system itself you may juggle population units at will, especially since almost all races have specific bonuses to production on certain types of planets.
4. Focus on colonising large nearby systems. At the beginning you should avoid systems with a large number of gas planets. Their high yield of one of the basic resources may be tempting, but it will be a long time before you acquire the necessary technologies that make these planets useful. Focus on planets with friendly environments, special resources or positive anomalies, and consequently ...
5. ... Begin with exploration! This will help you find out which planets may be even more valuable (or less). You can often find a lost population unit or a new module for your ships. Each exploration ship (with the magnifying glass icon) has several probes on board. They restock every few turns depending on the advancement of the module. You can send the probes to a planet with a curiosity or launch them out into the unknown (they will uncover terrain for several turns). At the beginning you will only be able to travel by using star lines between the systems, but given time you will unlock Free Movement for your ships, which will allow you to reach the most isolated systems. It is worth building several of these ships at the beginning of the game, and even creating a small exploration fleet in the process, which will make it possible for you to handle e.g. an unexpected pirate vessel.
5. In order to colonize you need a colony ship (usually). Most races use the classic colonization model: build a colony ship, send it to a given system, build an outpost, and help to develop this outpost until it becomes a legitimate colony. I wrote usually, because some of the factions have different methods of settling, but you will find out more about this in the descriptions of particular races. Unlike many other games, when you build a colony ship it does not drain a unit of population from the native planet! The outpost encourages migration or tries to "grow" its own population. Thanks to this, you can produce colonization units without fear of reducing your own population in your system. If you find that you have unnecessarily settled a given system - use the "evacuation" command. You will get a colony ship at the cost of the entire population and the improvements that you have already constructed.
6. Modules are the elements of each ship - armaments, armour or shields, additional equipment (engines, probes, etc.). You will gain more powerful ships not by unlocking a better unit, but by unlocking new, more advanced modules and installing them onto a ship. In a separate ship design menu you can decide on the quantity and quality of the invented modules. You can also discover new hull-classes of ships, which will often have more hit points and modules, as well as denser module slots (e.g. you can mount weapon modules in a given location, but they will count as double).
7. Another simple way to increase the power of the fleet is to increase the Command Points. Each fleet has a limited number, which affects the number of ships in the fleet. Only one fleet can face off against another fleet in a battle. Only after the skirmish comes to an end can another fleet join the fray. Therefore, even a small, but strong fleet can overcome several fleets of the enemy, one by one. Some technologies will allow you to develop this modifier, which will allow you to make up for the firepower by having a greater number of vessels in the fleet.
8. Pirates come from neutral systems belonging to minor factions. They will appear from time to time and circulate around the system looking for a fight. Until you conquer or assimilate such a system, their fleets will be created every few turns. Their quantity will be limited and the size of the fleet depends on the size of the neutral settlement. The more minor factions, the more such groups will travel throughout the nearby area.
9. Make sure to have the adequate administrators and admirals (heroes). It is better to have specialists than universal agents (although one or two "fillers" will always be useful). Heroes have access to many development paths, so check out all of the options and pick one of the two paths, that I am suggesting. The Admiral is a character, who will develop only fleet related skills and will lead your best ships into battle. The Administrator is a hero, who will focus on increasing the profitability and productivity of your best systems or of the ones which have just been settled (in order to accelerate growth). You may, however, assign one or two skills from the opposite branch of the skill tree, in order to make the characters more useful in times of peace/war.
10. Cold War - the diplomatic status you have with every newly encountered civilization. You can attack enemy fleets outside of their sphere of influence and block/invade their systems if they are within the range of your influence. This will affect your relationship with the given race. Increased generation of Influence (purple star symbol) in a given system can expand your sphere of influence. Thanks to that, you will not only gain a reserve of diplomatic currency, but you will also be able to take over the enemy system in a peaceful manner (or in the already mentioned military manner). In addition, if an asteroid belt or a nebulon field is within the range of the influence of your system, you will receive its respective bonus.