I haven't thought a lot of people liked Xenosaga, cool.
In my very limited experience, I liked the story of Xenogears, Xenosaga, Persona 3, Valkyria Chronicles (all of them), Wild Arms XF and Star Ocean games (only played the first three).
Game-play wise Xenogears was clearly not the best of these for me.
I will save this pages for future reference when I will have some more time for good RPGs, thanks for your suggestions.

ps: I haven't played those yet, but is Ateliers' series story bad in your opinions?

Xenoblade Chronicles!!

I have good memories from Grandia II too

SMTIV and FFVI (don't kill me).

Lunar Silver Star Story Complete
Suikoden
Suikoden II
Vandal Hearts
Final Fantasy IV
Final Fantasy VI
Final Fantasy VII
Final Fantasy VIII
Final Fantasy IX
Final Fantasy X
Final Fantasy Tactics
Tactics Ogre
Skies of Arcadia
Ni No Kuni
Grandia
Chrono Trigger
Xenogears
The Last Story
Lost Odyssey
Xenoblade Chronicles
Valkyria Chronicles
Vagrant Story
Dragon Quest V

...

There's just a lot, but to name a few:

- Chrono Trigger
- Secret of Mana
- Super Mario RPG
- FF6 to FF10
- Crisis Core FF7
- Ni No Kuni
- Xenoblade Chronicles

Nice to see a ton of love for Xenoblade Chronicles. Well deserved, one of the greatest games of all time.

Xenogears
Final Fantasy 6,7
Chrono Trigger
Dragon Quest 4,5

I'm also a big Skies of Arcadia fan!
Storywise, Dragon Quest 5 and Suikoden 2 are my all-time favorites.