1) I learned the concept of EV Training (and the interaction of Natures, IVs, and stat building, etc) way too late compared to other long time fans and players alike. After a LOOOONG hiatus of playing pokemon, to playing on the ADV Gen of RSE and FRLG, and I have played a ton of Romhacks since then. I didn't know about EVs until I realized that the fan game Pokemon Zeta and Omicron even made several points about it through the game's NPCs. In short, it took a FAN MADE GAME for me to realize its existence. So basically, the pokemon in the Romhacks I downloaded (Light Platinum and Liquid Crystal, both being very challenging romhacks in their own right) have all my pokemon with really bad stats. Now whenever i play a new file on a Gen 3 and beyond game, I carefully devote my starting time soft resetting till a get a starter with a good nature (I still haven't experienced the One try, Adamant Perfect ATK IV Torchic, but I did experience the one Try Mild Perfect Special Attack and Speed IVs Sceptile on Emerald)
2) Fennekin is my favorite Gen 6 Pokemon mainly for its appearance.
3) On my first playthrough of Pokemon Gold more than a few years ago, I didn't realize that the Red Gyarados was a special one-time only encounter, so I KO'd it because it was crushing my party.
4) I thought that Flareon was the best Eeveelution. Dear Sylveon i was wrong.
5) I didn't know about STAB back then. It took me a while to wonder why some moves, even if they are super effective against the other, aren't dealing the damage that I want to deal. Then there's that water pokemon NPC who's spamming Surf and dealing truckloads of damage even if its "not-very effective"
6) I actually believed the whole thing about Missingno killing your save file. I was wondering why my Gen I friends all had lvl100 Pokemon, with all the viable moves, and were already battling each other through link cable while I was still stuck leveling post-Mewtwo capture. Some of my friends still owe me their cloned TMs.
7) Back in Gen 2 G&S, I thought Sudowoodo was a Grass type, so i sicked my Quilava against the tree and i got surprised that my Flame Wheel didn't deal any damage.
8) Again, another young self Gen2 moment from me, I actually got swept by Bugsy's Fury Cutting Scyther and Whitney's Rolling Cow in my first attempts against them. I was really new to Gold and I was playing a Japanese cartridge of it so I had no idea what moves they were pulling off. *Japanese Text* Young me: Hah, that didn't deal damage. Second turn, okay that's still not doing damage, let me hit you again. 3rd Turn; WHAT THE HELL? What happened? All i saw was an animation and my pokemon suddenly got bursted down. 4th Turn; Really? One hit!?. 5th Turn: "....." It was even worse on Bugsy's Scyther. Once he hits that 1st Cutter, and he hits the 3rd, its pretty much a total party kill.
9) Aside from the red Gyarados, the only time I've encountered a Shiny wild pokemon in actual hardware (not emulation) was in Gold, where I saw a shiny Pidgey. I never realized the value of Shiny pokemon in Gen2 until a few years ago.