This might seem to be a game design issue, but it's utility is primarily for modder, so I placed it here.

In the original Endless Space, as in too many other science fiction strategy games, there was no easy way to mod the name sets. Stardock appears to be one of the few game developers to make this available (see mod abilities for Galactic Civilization II and III). The common areas for renaming are:

• Star Names:  Allow modders to substitute a new list of possible star names, instead of the default list, and make the list variable length. For example, some people like to use "realistic" sounding actual names ( https://en.wikipedia.org/wiki/List_of_proper_names_of_stars ), Bayer Names ( https://en.wikipedia.org/wiki/Bayer_designation and https://en.wikipedia.org/wiki/88_modern_constellations ) and/or Flamsteed Names ( https://en.wikipedia.org/wiki/Flamsteed_designation and https://en.wikipedia.org/wiki/Table_of_stars_with_Flamsteed_designations ). Others prefer names from their favorite science fiction novels. 
  • NOTE: Having a "duplicate detection" algorithm for duplicate names helps. I suggest using a variant of modern astronomical conventions. If the name already exists, just add an alphabetical letter after it, such "Essa" and then "Essa A," "Essa B" etc. This isn't great, but it's better than having the same name for two different systems.

• Ship Size Names: It is typical for designers to "lock in" ship size names, such as "Destroyer", "Cruiser", "Dreadnought" etc. However,  even in modern navies, there is no commonly accepted convention. For example, modern American "Destroyers" are often larger than "Cruisers" built a few decades ago. Furthermore, modern naval designations differ somewhat from those of World War II (the term "Destroyer Escort" has fallen out of use, and the term "Frigate" moved into more common use). This in turn can differ from World War I (where the terms "Dreadnought" and "Super-Dreadnought" were in common if not official use), etc.. Ship size names were significantly different in the age of sail (Sloop, Brig, Frigate, Ship-of-the-Line). It can add a lot of flavor to mod just the names for different ship sizes.

• Individual Ship Name Sets (within a type): Allowing players to name each ship built is a nice feature, but giving them the ability to assign a "name set" to a class is also nice, and commonly done in naval circles. Game logic would select one of the names within the set for each ship built. Examples of name groups used historically include:
  • Alphabet Classes, such as interwar British Destroyer classes: "A" Class (Active, Ardent, Arrow, Anthony, etc.), or "B" Class (Beagle, Basilisk, Brazen, Brilliant, etc.), or the "In-" battlecruisers (Invincible, Inflexible, Indomitable, Indefatigable)
  • Regional Classes, such as British Counties (Suffolk, Norfolk, Cumberland, Cornwall, etc.), American States (Arizona, Nevada, Missouri, Maine, etc.) , Japanese Provinces (Nagato, Yamato, Fuso, etc.)
  • Geographic Features, such as Japanese Mountains (Akagi, Chokai, Iwate, Myoko)
  • Animal Variants, such as those used for Japanese WWII aircraft carriers (Flying Phoenix, Great Phoenix, Fortunate Phoenix, etc.)
  • Weather Conditions, such as  those used for Japanese WWII destroyers (High Tide, High Wave, Crescent Moon, Snowy Wind, Evening Cloud, Twilight, etc.)
  • Plants, also used in Japanese WWII destroyers (Pine Tree, Spring Grass, etc.)
  • Hero Names (reuse the names of various heroes in the game, or heroes that have been hired by that faction)
  • Star System Names (reuse the names of player-colonized star systems)
  • New Name Sets: Allow the player to create one or more new name sets, including the title of the set, and the names within it. 
  • NOTE: Sometimes there are more ships built than names in a name set. While there are many ways to resolve this, I recommend adding a incrementing Roman Numeral each time the name set recycles. For example, after a name set of four mountains (Akagi, Chokai, Iwate, Myoko), the next ships names would be Akagi II, Chokai II, Iwate II, Myoko II, then Akagi III, Chokai III, etc. Again, this isn't great, but it's better than having the same name for two different ships.

• Hero Names: Separate the hero name from his or her stats (attribute data), so that modders can rename heroes without changing the game balance.

I'm sure other areas for minor customization will come to mind, such as battlefield tactic names, ship equipment terminology, etc. 

WHY BOTHER?  I know that some game designers want to exercise their own creativity, and communicate certain concepts through naming.  This should be a tip-off that modders will want to do the same. Modders like to put their personal "stamp" on the game. Every player who mods your game, regardless of how minor, becomes a more engaged and loyal customer, as well as an advocate of your product to other gamers. The professional designers of Amplitude have already had their say - by assigning the default names. Let the players have a bit of fun too.