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.
Sequel Displacement: If you are familiar only with the freeware The Ur-Quan Masters, you might be surprised to know there was a first installment.
Star Control II
Computers Are Fast: The AI uses some secondary abilities with frame perfect accuracy too often. Syreen ships will trigger their song the moment they get in range. Utwig and Yehat ships raise their shields the instant they get hit and drop them right after. Shofixti Scouts never mistime a Glory Device detonation. It is a very good thing all of those are mostly on your side during the campaign...
Demonic Spiders: When exploring planet surfaces, you'll usually be able to beat any creatures you encounter even before you acquire any lander upgrades, provided you have enough skill. Not so with Fungal Squids. Even though the damage they cause is only classified as Moderate, they are a lot faster than your lander, have quite a lot of HP, and are hunters (which means they will chase your lander relentlessly until either you or the Squid is dead).
Slylandro Probes, which you will encounter very frequently. The only hard counter against them is the Chmmr Avatar, which you don't get until near the end of the game. Until then, the best counter is usually your own upgraded flagship, which exposes you to a lot of crew damage.
Draco in Leather Pants: Admiral ZEX has become much more popular in certain sections of the fandom than was ever originally intended.
Nightmare Fuel: "They have names, but you do not know them. They would like to find you but they are blind to your presence... unless you show yourselves. The Androsynth showed themselves, and something noticed them. There are no more Androsynth now. Only Orz."
"JOKE. YES. HERE. IS. A. JOKE."
The gruesome descriptions of what the Ilwrath do to their captives.
Play the Game, Skip the Story: Defied by the second game's design. If you don't pay careful attention to the dialogue, you won't be able to complete the game.
So Cool It's Awesome: IGN named it the 17th greatest game of all time. Gamespot also named it one of the greatest ever.
Tear Jerker: The Taalo were explicitly stated to be immune to psychic powers. That psychic shield they left behind wasn't for them, but for their Ur-Quan friends, to free them from the Dnyarri. But the Ur-Quan never found it.
Unwinnable by Insanity: Go to an enemy planet protected by an infinite fleet without your emergency warp escape unit. Lampshaded by the Thraddash, who keep score of how many of their ships you have destroyed, except for fights in their homeworld. Even they think that's incredibly stupid.
Run out of fuel and keep refusing contact with the Melnorme.
As noted on the main page, attempting to complete the game without ever making contact with the starbase was impossible. The Ur-Quan Masters made it inhumanly hard and tedious.
Star Control 3
Game Breaker: The Doog Constructor ship, especially with the upgrade. The main weapon automatically points towards the enemy, and the secondary ability is a self-repair system.
Special Effect Failure: The Harika is eating the Yorn! No, wait, a puppet is holding another puppet in its mouth... and now it's back in his pocket.
All the other puppets, from the unsexy Syreen, the vile, Chucky-like Arilou or the lazy-eyed Exquivan also fall under this trope. Not helping anyone's case is how poor the animatronics for each character is.
Paul Reiche III: However, the Syreen should ALWAYS be sexy and strong. The image of them in SC 3 was spooky and unpleasant.
Values Dissonance: The Harika and Yorn. The Harika don't find it odd at all that they eat the sentient Yorn, while the player (As well as anyone who isn't into Vore) finds it...disturbing. Especially once the Yorn finally pops up and says "We like being eaten" and that they view it as exaltation and only go to be consumed if they want.
Vindicated by History: A rare inversion. When it launched, SC3 was given several high scores and was a critics' darling. Nowadays, not so much.