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Federation Starfleet: Generalist, they have a wide variety of abilities but lean on the defensive side in the interest of keeping ships alive. A Commander Is You: Most of the time the sides have similar tech trees and vessel types with variations in each unit's stats and their abilities if they have them. This is in the interest of allowing the player to have a Superweapon when playing as the Federation without needing to resort to weapons of mass destruction, as well as giving the Federation a superweapon that fits their overall code of conduct (not resorting to subspace weapons, and time stopping having other applications besides warfare.)
The Federation almost ignores the existence of the Temporal Accords, and outright uses Temporal Research Facilities to generate Manheim Effects which freeze time in a large radius and allow their ships to engage without any return fire.
The No Warping Zone within gravity wells is all well and good for most Sci-Fi but it's at odds with the series proper as ships have been shown to be capable of warp speed near planets or other bodies.
You would think Rule 9 note opportunity plus instinct equals profit would attract every Ferengi and their mother Rule 31 never insult a Ferengi's mother, clamoring hand over fist to mine it for themselves.
Latinum can apparently occur naturally in nebulae which can be mined and processed into GPL as a trade and research commodity. Also notable is the prevalence of traversable wormholes - something that was so rare in canon that only one is known in the galaxy. Well Star Trek reality - if the Federation really had the ability to churn out Sovereign class battleships as quickly and easily as you can in game then the entire franchise would be radically different. 2-D Space: Played straight in the first game but this gets Downplayed in the sequel where you can move units and build stations above or below what the game calls the Zero-Grid, this does not allow you to build stations above or below each other.
Both games will soon be available at GOG.com if you'd like to play them.