I remember misconceptions I had with three Pokemon and their typings. Coincidentally, all three are Gen III Pokemon:
1) Let's start with Glalie. With those horns and that intimidating face, it surely had to be a Ice/Dark, right? Well, I use a Fighting attack with Hariyama and it's super-effective as I expected... then I realized Fighting was super-effective against Ice.
2) Flygon. Picture ~12-year-old me seeing it in the battle against Drake. Well, I didn't have Ice or Dragon attacks so I go with Thunderbolt, since it's neutral on all Dragon/Flying Pokemon. "It didn't affect enemy Flygon...". What. I lose, so when I try again (thank Mega Rayquaza for save states :P) I try with a Ground-type move as I had sent Swampert out... and I find out Flygon was Dragon/Ground with Levitate. How on Earth was I supposed to guess that!? Let alone the fact it's Trapinch's final evolution.
3) Rayquaza. I see the plates on its chest and I think "Dragon/Steel". Nope, Dragon/Flying... but I chuckled a bit when Dialga appeared with a Dragon/Steel typing.
In regards to design alone... I remember thinking Torkoal was far bigger than it actually was. Its RSE sprite was really misleading.