* AWinnerIsYou: The ending is just a single splash panel of world leaders celebrating victory. Even the original X-COM for DOS, working on more limited resources, had several of them, telling an actual story.
** After version 1.5, there is a long and detailed description of what happens: All alien captives fall into a coma, and your military advisor tells you that you should neither turn over your equipment to the United States, nor the Soviet Union, but to unite a new Earth free from prejudice and broken political systems.
* BrokenBase:
** Are the graphics unacceptably bland for a 2010s game, or is their plainness and simplicity the very thing that makes them appealing compared to the flash of ''VideoGame/XCOMEnemyUnknown''?
** Was it right to leave out [[spoiler:psionics]] and the Blaster Launcher?
*** Blaster Launcher still exists, albeit weighing a whooping 50kg, using an incredibly rare alien engine, and 500000$, making it unable to be used by anyone except soldiers in power armor with a huge bank account. And is useless.
** Mechanical fidelity to the original is one of the selling points, but some think it's ''too'' faithful, WithThisHerring and all.
* DemonicSpiders: Reapers. They can move absurdly far, have a OneHitKill attack that creates another Reaper from its victim, and almost always come in large numbers. If you don't run them down quick on terror missions, you'll be facing a ZombieApocalypse in no time flat.
* DevelopersForesight:
** Considering that the timeline starts in the middle of the UsefulNotes/ColdWar, where resources are usually scarce and trying to be accepted by both sides of the world from Communism to Capitalism is what the Xenonauts start off with, [[ShownTheirWork it's likely the case why funding was quite low during the beginning of the game]].
** While the Rocket Launcher stays in regular condition, [[spoiler: its rockets evolve along with the technology as the player progresses, from regular explosives to alienated chemicals to [[PlasmaCannon plasma]] blasts]], the existence of Blaster Launcher may no longer be needed.
** [[RealityEnsues Again]], UsefulNotes/ColdWar, which leaves the ideas of powerful mech units for players behind... [[spoiler: to replace them by PoweredArmor with an active inventory, providing the soldiers greater versatility than X-Com would have provided]].
* GoodBadBugs: If you leave an injured soldier in your base to recuperate, it will take many days. However, sending him or her into battle again and using a simple medikit fixes the problem instantly.
** Now no longer in play as of v22 Experimental 5, as sending troops out wounded now caps their maximum HP during the fight.
** It used to be possible to have soldiers DualWield...''shields'', who could '''still''' throw grenades and smash aliens with kicks while doing so. Not a StoneWall to be laughed at.
* JustEatGilligan: The final mission involves boarding the alien's main ship while it descends to start a ZombieApocalypse with a horde of Reapers to kill the alien leader on board. While this main ship is presumably strong (it's classified as a dreadnought, the biggest UFO's you can dogfight are battleships), you're not even given the option to just shoot it down with fighters. There's no reason the otherwise AwesomeButImpractical X-120 Fury couldn't vaporize the dreadnought with its [[WaveMotionGun Singularity Torpedo]]. But then there wouldn't have been a climactic final battle.
* MemeticBadass: Josh Eales. Because of an [=RNG=] bug, this name was always in the starting party of every new game. Now he even has his own Steam card.
* TheyWastedAPerfectlyGoodPlot: The Cold War setting is little more than window dressing and plays no part in the plot of stopping the aliens. It certainly would have been interesting to have deal with not only the alien invasion, but keeping tensions between NATO and the Warsaw Pact from spilling over while they fight over who gets the spoils of downed [=UFO=]s.