I have to preference this with the fact that I have played all these games so these are first hand opinions.
PS2 - Xenosaga Episode III: Also Sprach Zarathustra
Of the 3 titles in the series this one is my personal favorite overall. In terms of visuals, pacing, overall gameplay and combat this was the peak of xenosaga imo. Since you already have the first two this should be an obvious choice. It does feel a little rushed since the series was originally supposed to have 7 installments, but it still holds its own regardless. I am currently working on my 2nd time through this entire series.
PS2 - Stella Deus: The Gate of Eternity
As far as tactics games go on the PS2 this one is by far the most user friendly and least technically intimidating. Unlike titles such as phantom brave, la pucelle, and other NIS tactics games this titles does require obsessive attention to the leveling systems or in items in stats. The alchemy system in here is also not central to finishing the game, but rather makes the game easier and adds depth, not difficulty. I still find myself periodically popping this back in just to mess around with because it is so well done.
PS2 - AR Tonelico: Melody of Elemia
This game falls into a unique category, and yet is fairly similar to the altier iris games in terms of gameplay. The story here, albeit bizarre at times, is quite unique and entertaining throughout. Another bonus is if you hate spending time and grinding, not once when playing this game did I have to stop to level for a boss or a new area. A major plus since you end the game at 75+. The alchemy system is fairly involved in this title (making it similar to the altier iris titles) but not overly difficult to pick up. The battle system is also very slick and the side plots in this game are great stories in there own right. Who doesn't want to dive into the mind of party members.
PS2 - Magna Carta: Tears of Blood
This game is a mixed blessing. The game features some of the more beautiful graphics you can find in a PS2 title in the US. Character design, as well as monster/bosses are usually stunning if not near breathtaking. This comes at a cost however. The game takes forever, and I mean this in multiple ways. Half of your time is spent in load screens, which isn't much of an experience. Whether it be for battles or changing maps. The battle system is also slow and clunky, as you are constantly managing natural magic in the area. It adds a unique challenge to the game, but i felt it detracted from it overall and further slowed this title down. This is a title i still haven't completely finished. If you dont' mind long load times and slow pacing this title isn't terrible, just a long investment.
PS1 - Vagrant Story
Personal opinion, stay away. THis game had some great concepts, such as weapon resistances and monster specific strategies. You had to carry multiple weapons to be prepared for whatever jumped out of the dark. While it was a thinking game and kept you on your toes, I felt it was so cumbersome scrolling through what seemed 20 weapons just to beat down a skeleton. I still don't quite understand why some people like this game so much, but it is there choice.
If I may suggest some titles (I have no idea what you have played or own, so forgive me if i stumble across one)
PS2 Soul Nomad
If you played ogre battle 64, or know of it, think of this as the unoffical successor. Tile based teams are set up and run across the tactics style (as opposed to real time in OB 64). The units then meet and pummel each other, which is fairly standard. The game shines however in the custom abilities you can get by mixing and matching the dozens of unit types. Coupled with the accessories and options for post game madness (think disgaea with the outrageous level options) it is a solid title.
PS2 DIgital Devil Saga 1 + 2
One of the darkest rpgs out for the PS2. It is set in a post apoclyptic world with demons and magic. This game is not for the faint of heart as the game itself is quite difficult, i.e. random battles can wipe you if you aren't paying attention. THe plot however is deep, interwoven, and very unpredictable. If you can handle the difficulty curve and the heavy handed violence a great story with an engaging cast awaits.
PS1 Parasite Eve
I saw that you didn't prefer games where guns are used, but this is still a great game. The plot, while glaring inaccurate (i know too much biology) is still great, if a little gory. Of the ps1 rpgs the graphics are above average (Far better than FF7). THe game is somewhat difficult, below Digital Devil Saga, but will definitely challenged the pummel boss and heal routine you see so often.
Hope this helps. I have a much greater depth of knowledge, but I thought this might help you out. If you have any questions, just send me a pm.