These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ear Worm/Crowning Music of Awesome: For just three tracks in the series that plays every start up in the respective titles, players get this feeling. Two of them were original, Nova however, uses Mars, The Bringer Of War by Gustav Holst, an eight minute track for a loading and menu screen that last about six or so seconds. (Presuming you don't read the intro)
Fandom Berserk Button: If you spell "Vell-os" any other way, with any other capitalization, on EVN forums, you will be rather pointedly corrected.
Federation, Auroran, and Pirate ships are pretty evenly matched (a forum member reported he once took out a Federation Carrier using a mass-moddednote start with a decent size freighter, then convert the majority of the cargo bay into room for weapons Pirate Enterprise rigged for More Dakka), but Polaris ships eat them all for lunch. In particular, the Feds and Aurorans have absolutely no counter for the Raven.
Also the Manta, mainly because it's the only fighter in Nova that can do appreciable damage to capital ships without modification. In addition to being blindingly fast and agile, it mounts a Bio-Relay Laser, which is easily a light capital ship weapon.
Supposedly (going by the in-game ship description) the Federation can counter at least the Polaris capital ships using the unlockable RAGE Gunboat. In practice however it's just an uninspired heavy fighter whose ill-defined "reactive" armor ability does little to protect it.
In Nova, you can run luxury goods from Europa (Medium price) to Earth (High price). Not game breaking by itself considering the low margin, except for the fact that they're both in the same system. An hour or two of doing this and you'll have all the credits you will ever need.
Out of the incredible Polaris arsenal, the Polaron Torpedo is particularly ridiculous. It's fast, does enormous damage, can't be stopped by any other race's countermeasures (both jamming and point-defense systems), has near-perfect tracking and lasts for far longer than any other secondary weapon before burning out. It doesn't even take up mass, so you can carry dozens of them on even a gunboat. Of course, if that wasn't bad enough they also get a version for capital ships which releases several of the damned things at once.
Good Bad Bugs: The "Machine Gunning" bug causes the Vell-os Summer Bloom attack to be more powerful than programmed In Nova, and more efficient than Winter Tempest.
Mary Sue Topia: The Polaris civilization is centuries more advanced than its neighbors, has a caste-based society which operates in near-perfect harmony, is almost entirely free of the piracy and internal dissention which plagues the other factions, and has a ludicrously powerful military whose fighter craft can feasibly take on capital ships. Their ending implies that they literally all become Gods.
Friendly faction ships (not escorts) will be all too eager to blow up that Kestrel you've painstakingly disabled after several minutes of combat. Similarly, escorts can be overzealous in missions that require you to disable but not destroy your targets.
Escorts can be ordered to disable ships but they will not stop firing until the ship is disabled. So if it takes a couple of seconds for missiles to reach the target there will be a couple of seconds worth of Macross Missile Massacre on it's way to destroy the ship.
That One Level: "Distract Moash" in Nova. You need to land on a space station while not letting too many of your escorts die. Between you and the station is a massive amount of Moashi ships. You're likely to die from gunfire before you can slow down enough to land.
Most fun solution is to save this mission for late in the game, when you can take on the enemy fleet single-handedly. Nova has regrettably few scripted opportunities to fight so many powerful ships at once.
They Wasted a Perfectly Good Plot: Or at least a Perfectly Good Way To Make Money. The official timeline for Nova mentions that scientists discovered the chemical TCTLIDS in deep space, then created the narcotic FATE accidentally when they tried to make medicines with it. But no mention of TCTLIDS or FATE is found in the game files.