I've always found these threads fun, both in what we can come up with, and the discussions it creates.
Because I'm lazy, my first post will be copypasta of what I've listed b4 in other forums.
1. Why is it that when a character is hanging from a cliff and is gonna fall, there's never a timer for you to save them? I mean, you're given all the time in the world while the person is HELPLESSLY DANGLING OVER A DROP THAT WILL KILL THEM.
2. Why is a hero incapable of having a hometown that isn't ransacked/burned/the people slaughtered? Would it kill the hero to have a normal life before he sets out on his journey?
3. If Lavos encompasses all periods of time, why didn't he just bring hundreds of himself from different points in time and utterly crush Crono and the others? Or hell, why didn't it, after merging with Schala, just use its powers to tell its past self to shoot a bunch of explosive spikes and destroy Truce the day Crono was born, killing him and erasing his existence?
4. If the hero is a boy, why is his dad always dead? Not only that, but if it says how he died, why is it always in a really pussy and underhanded way?
5. Why do people like Squall, who are completely clueless about women, have all the girls in the game falling in love with him?
6. Once again, why do all RPG heroes, in a world of guns, use swords? I understand the whole "skill" behind it, but get with the times people! It's an archaic way of fighting that simply can't compare to modern firearms. In real life, if a person with a sword fights fairly a person with an Uzi, 95% of the time, the guy with the Uzi will win 3 seconds after the fight starts.
7. How does Wakka's blitzball always come back to him?
8. How come no one ever drowns when playing blitzball?
9. Why do level 30 guards need your help in killing level 10 monsters?
10. Why don't NPCs ever give that one piece of information you actually need?
11. Why doesn't the hidden monster who's way tougher than the final boss ever decide to just kill the final boss and take over the world himself? He could probably pull it off!
12. Why are all the Dark Side powers so much cooler than the Light Side powers?
13. Why do all female villians reform their ways, or at least redeem themselves before dying? Are girls less capable of evil or something?
14. Why did Cid give you that lamp without bothering to tell you that the devil was inside it?
15. Why does time travel never make sense?
16. How come I can come up with a logical solution to a problem in like 5 seconds, when the hero tends to come up with a vastly overcomplicated one with a high chance of error?
17. Why doesn't the hero ever just stab/shoot the villain during his monolouge? You wanna know his motivations? Search his room and read his fucking journal!
18. How come Guybrush is able to fit all that stuff in his pants?
19. How come games with ship battles never have a chain-shot to fire, despite how easily they cripple enemy movement?
20. How come ranged weapons are more accurate than melee weapons?
21. How come anime games are only good in the fighting genre?
22. Why was Manny so reluctant to say how he died? He was hit by a train, big deal!
23. How come there aren't enough hard games anymore?
24. How come there hasn't been a Monkey Island 5?
25. Why are Carriers so overpowered?
26. Why does the villain decide to stop the creator of his weapon by locking him up (since he knows how to destroy it)? Why doesn't he just kill him?
27. Why do all dwarves sound Scottish? Especially considering that the earliest known stories about dwarves were Scandanavian.
28. Why do villains never kill you when they have the chance?
29. Why does the hero always show mercy, even if the bad guy in question killed his parents, siblings, burnt his house down, skinned his pets alive, and gave him AIDS?
30. Why don't heroes ever stick up for themselves? If you're accused of a crime, don't just stand there trailing off like an idiot. Defend your innocence you maggot!
31. Why does no one in games ever have to go to the bathroom?
32. Why do guards never take your weapons or armor when they lock you up? Even when they do, it's in the next room, guarded by just one guy.
33. How does killing the minions in Shinobi let you do more damage to the boss? The life energy doesn't get absorbed by the sword until AFTER the final guy is killed, so it's not like you have the energy stored up to hit him with.
34. Why do you bother to fight the boss in an attempt to stop his summoning of the super-monster if he always succeeds in doing so after the fight anyway?
35. Why is the past always more advanced than the future?
I can think up more, but I wanna see what other people come up with.