I've just beaten Final Fantasy VII, VIII, and IX for the gazillionth time and I've got to say the best Final Fantasy for the PS2 is IX. Here is why.
Let's start with the characters. The main character, Zidane Tribal, is totally different from previous main characters, even in the NES and Super NES Final Fantasies. Zidane has a cocky, perverted, and upbeat attitude, yet he has also shown compassion, leadership and commitment towards his fellow companions. In Final Fantasy VII and VIII, the characters involvement in the game seemed very little. In VII, the whole focus was on Cloud, Tifa, and Aeris, while the rest of the characters were basically ignored and just there for battle purposes. Same thing with VIII. We don't see huge importance in characters like Zell, Selphie or Quistis. The whole story revolved around Squall and Rinoa. In IX, we see how each characters develop during their journey with Zidane and see the importance of Zidane's involvement with each character's problems. Every character in IX starts off with their own unique flaws. Zidane changed Steiner's loyalty towards one person to a whole kingdom. He showed Amarant the importance of teamwork. Eiko, who was always alone, found the meaning of friendship and love. We also see interactions between the sub-characters as well. The master and servant relationship between Vivi and Steiner, sisterly bond between Eiko and Garnet, rivalry between Freya and Amarant (which made the realization of the importance of teamwork so much more powerful during their fight with one of the 4 guardians). There was even a little love triangle between Zidane, Dagger, and Eiko. We also see that Zidane isn't so perfect either during that powerful scene at the end of the 3rd disc. Zidane, upon learning that his sole purpose was to destory everything he loves and cherishes, falls into depression. It was great how all the characters Zidane helped helps him in the end.
I also loved how IX took it back to the whole medieval settings. When I think of Final Fantasy, I think of swords, knights, castles, princesses and such. It's great how VII and VIII had the whole futurific look because it worked for a lot of people, but it just didn't make sense to me that a motorcycle and a chocobo exists in the same Final Fantasy world since they would both have the same purposes.
I've always loved the job class system in Final Fantasy. It worked so well in IX. We would think that job classes are only important during battles, but I thought it was awesome how great it worked with the storyline as well. It is highly unlikely that a lowly thief would be the main character in Final Fantasy. It's usually the Cecil and Terra who is chosen as the main characters. By Cecil and Terra, I mean characters who are highly powerful and has a reputation.
I don't think any other Final Fantasy can compare with the soundtracks of Final Fantasy IX, not even X. I thought the songs were highly memorable. I can still remember the tune for each town because it fit the settings so well. The Lindblum town always had that "another long day of work" type of tune. It matched the whole low working class theme of Lindblum. Treno which represents the town of nobles and the city that never sleeps had the whole upbeat, classy, night life theme to it. Some of my favorite tunes were Loss of me/Rose of May (because it just reminds me of the scene where Steiner and Beatrix worked together to protect Alexandria), You're not Alone (because it's just so epic), Daughter of Madain Sauri (because its very happy and it feels very...Eiko. Although she was very sad in the inside, you would never guess with this tune), and of course the world map theme (because it sounds so adventurous).
The battle system in IX was ok. I thought VIII had the best battle system. I loved the whole junction system, but IX's wasn't bad. It just seemed too...normal.
Oh and let's not forget, the best villain, Kuja. Not Sephiroth. I thought Sephiroth was very over-rated. Yes, he killed Aeris, but he accomplished nothing. Sephiroth just went on a rampage and such, but Kuja seemed more cunning. Manipulating Queen Brahne, kidnapping Dagger, and creating black mages and creating havoc within Gaia destroying half the planet. Wait, let me fix that. Destroying a whole planet (Terra) and a half.