Uh this isn't one I ever used, but I used to hate Azelf Mespirit and Uxie. i thought their designs were bland and I hated that they were all the same type despite being a legendary trio. However, after hearing their battle theme recently, (best song in the series in my opinion) seeing their pokedex entries and after reading the Adventures/Special manga, I realized how freaking amazing their concept is. They're based on everything that shapes us as human beings. I especially love Azelf, as willpower is so important to everything we do.
"Resolve is everything. When one tries something, it ends in success or failure. But it is in the attempt that one will see true value."
Also I hated Trubbish and Garbodor, but damn Trubbish is cute.