Same here about the Honeybee Inn. I had no clue what was happening there. Giggling girls? All those embarrassed dudes outside? A bunch of guys in a bathtub? Whaaa--? Oh, sweet naivety.
Don't know if it fully belongs here, but discovering that the infamous LTD was a thing was shocking and slightly disturbing. I always thought that Cloud and the girls were simply best friends, no romance whatsoever. I still love to think they are (at least in the OG). Either I'm blind or I cherish the power of friendship way too much, so I take advantage of the game's ambiguity... *sigh* Also, I always thought that Cloud and Tifa simply fell asleep watching the stars under the Highwind... I still love to think they did, because it's just incredibly inspiring, isn't it? *heavy sigh*
I could never be bothered to fight Ruby and Emerald Weapons.
Some aspects of the storyline used to be incredibly confusing, and it took years of gaming, reading extra materials, studying the compilation titles and gaining life experience in general to put all the pits and pieces together. And there are a couple of things I still don't understand, but maybe they are just plot holes after all.