I suppose you already know all the other good FF games, so I won't mention any of them here right now and instead focus on other franchises. When it comes to deep storylines that carry important real-life messages and feature generally well-rounded characters, the best ones I've experienced in my many, many years of playing JRPGs so far include (in no particular order):
Xenogears - perhaps the only other JRPG story I'd place on par with (if not slightly above) FFVII, and that certainly means something. Developed by Squaresoft, before they fused with Enix.
Vagrant Story - another good old Squaresoft game. Short but good (if you can get used to certain gameplay mechanics, that is).
Chrono Trigger - yet another Squaresoft game, and an all-time classic for most people who know it, and for good reason. Only drawback is the silent protagonist, but all the other characters are well done.
Tales of Symphonia - don't let the colorful anime style fool you, the game is much darker than you'd think. The story's complexity with its many well executed plot twists and proper use of foreshadowing can certainly draw you in.
Tales of the Abyss - much in the same style as Tales of Symphonia. Again, if you don't mind the anime-like style, you'll be rewarded with a story featuring extensive World Building and intelligent plot twists.
Suikoden II - A highly political, yet also highly emotional story. Much more grounded and real life oriented than most RPGs. The only downsides being the silent protagonist and the really shitty translation.
The entire Wild Arms series. Much like Tales of, when it comes to World Building, thematic content and overall narrative, the Wild Arms team certainly had some talented writers.
There are certainly more, but those are my personal favorites.
