Final Fantasy IX is my favourite in the series. I liked the varied cast, yes even Eiko and Quina of all people. The soundtrack is very beautiful and the pre-rendered backgrounds still look pretty good, not to mention that the game's world has alot of interesting locations you get to visit, like the Iifa tree, Millennium palace, Ipsen's castle and Oeilvert. I also have a soft spot for the art style and it's super-deformed character desings, but despite it's "kid-friendly" look it managed to tell a really deep story that dealt with some heavy themes.
My vote goes to Final Fantasy VII. Here is the reason why? Final Fantasy VII has a large well built story line that made the game so interesting. It's unique Materia System allows the player to equip and combined the materias to create different combinations. It also has a character switch system that allows you to switch characters from your party.
The soundtrack of this game is very solid since it has a numerous of great songs in it. The 3D graphics was quite good at that time. The game also contains a lot of Side Quest, Hard Core Bosses, etc. That is why I voted Final Fantasy VII as the best game of the series.
Once you hit FFVI you realize every FF has a system that let's you change your party right? There is nothing unique to VII about that so it doesn't really make it stand out at all.
Most Final Fantasy game has a character switch system, but not all of them work the same. Each of their character switch system has a unique way of working. Some of by a save point and other by the menu. Let's look at Final Fantasy X as an example. It's character switch system allows the player to switch characters while in battle. It's function is different from the other Final Fantasy titles .
The PHS also gives you access to set the character's position in battle by setting them in the front or in the back row. That is something that fit well with the game since you can use it as your advantage.They actually don't all have a unique way of working to that extreme, since you mentioned X I can easily counter that. It's not just limited to the battles, after battle you can change order as well through the actual menu. All of them include going to a person or area to usually change the core makeup of your party. The thing seven did differently and you didn't even mention that aspect was the PHS which allowed switching at save points. You only mentioned character switch which has been a staple in VI and beyond, not a unique switch but just character switch.