Honestly, a -lot- of hate for FF9 stems from the character design. The main character is a monkey-tailed 80's glam rock star, there's a big knight with gratuitous eyeliner, and your dragoon is a rat. Also, Kuja looked pretty fruity for most of the game.
All that said, I loved that it has been the last character-defined-class game (IZJS 12 not included) since like... 4? 6 to a degree as well, even though most special abilities go to the wayside once you get certain relics and spells from espers. And personally I really liked the fact that it was basically a love letter to the pre-PS1 games, with Vivi being the most obvious. I liked the equipment based skill learning stuff too. And the fact you actually had equipment slots for shit, unlike 7 and 8.
Necron was... well, Necron. Basically the anti-crystal in the game, but yeah he's not even really mentioned until you are just about to fight him. And admittedly, I beat him by accident because Zidane was my primary attacker guy with mp-attack and some other crap. Well, apparently, when berserked he does retarded amounts of damage, and with auto-haste he literally just straight rapes. Everyone in my party died but Zidane, who got hit with berserk right before, and Zidane proceeded to solo Necron. Definitely not my favorite end-boss to a FF game, and he wasn't even extra content.