Dialogue options that effect gameplay and story
Exploration
Puzzle & adventure game elements, ideally at all times (included in the story segments as well as dungeons)
Extensive Party/character building RPG systems allowing for lots of freedom of choice & strategy - stats, abilities, perks, whatever.
Optional shit (secrets, side quests, mini-games)
Strategy (party formation, certain battles requiring certain builds, item management etc)
Navigation challenge (where to go next, maze-like level design etc).
Combat at the center of it all.
FF is this.
Which Final Fantasy had "Dialogue options that effect gameplay and story"?
Anyway for the thread, Breath of Fire 2/3/4 may fit, they all have a fishing and town building mini-game, which rewards you with good equipment, Breath of Fire 2 had the Fusion side content, fusing characters to get stronger characters, and you had to explore to find the witches to allow different fusions. Breath of Fire 3 and 4 have the dragon forms side content as well. In 3 and 4, you also had the teachers who could change your characters build and gain different abilities. You could learn abilities from monsters as well. And two different endings depending on your choice at the final boss. Lot to explore and find in these games. Breath of Fire 1 as well but i kinda of hate that game, most bland combat ever.
Lufia 2 had the roguelike Dungeon, endless replayable and could reward you with good loot, there is not a lot of incentive to do so since the game combat is really easy, but some romhacks might help it that. The game also had pokemonish side content, with different monsters to raise to help you. Lufia 2 is famous for its dungeon puzzles, which are the best part of the game.
When it comes to exploration, the best i've played so far is Golden Sun The Lost Age, so much backtracing to find secrets, new abilities that unlocks new secrets and so on... almost open world. The entire game is about is about gainning new abilities that allow you to get into places you could not before, so its like a Metroidvania in JRPG form. Lots of secret bosses and the difficulty is just right, for the bosses at least, random encounters are pretty easy. Lots of puzzles, lots of secret bosses, lots of optional djnns. A baldur's gate 2ish crafting system. Some character customization. There is a Hard Mode, but sadly only after completing the game. Fantastic game in my opinion, i'm not a fan of the first game though.
Star Ocean 1 on SNES had a robust character customization, after levelling up, you had a lot of skills to chose where to put your points on, from cooking to crafting to alchemy to combat skills.. there is a lot. The game have a lot of optional recruitable characters, as well as dialogue options and other optional content and so on... The game does not hold you hand when it comes to exploration, i got lost a lot of times, in fact right at the beginning of the game i found a secret dungeon where i got one shotted by the enemies there. I heard there are different endings as well. I haven't beaten the game but from what i played it fits you criteria. And i assume Star Ocean 2 is the same, and i heard that game has a lot of optional content and 50+ endings, so even more so.
Saw someone bashing Suikoden, and i agree it's not deep gameplay wise, but for exploration, the incentive is to find new recruitable characters and how to recruit them, that's why i never did and you should not play with a guide, of course i never came close to get all the characters to get the "good" ending but the "good" ending kinda sucks anyway, so i wouldn't and you should not bother with it. I've played Suikoden 1 and 2 multiple times and on replaying it i recruited new characters i could not before, and even side quests, so there's a lot to explore there.
Dragon Quest 3 on SNES is one of my favourites ones, it has character creation like FF1 except for the main character who is always a Hero, but there still a lot of character customization from you heroes to the party members, you could change the characters personalities after reading a book/tome or sometimes wearing specific itens, these personalities change how much and what attributes you characters gain after leveling up, these books/tomes are hidden all over the place, you need a wiki to understand their effects on characters though:
https://dragon-quest.org/wiki/List_of_personality_types_in_Dragon_Quest_III ,but don't read where to find the books/tomes or you would spoil the fun. You could change party members classes later on, kinda like a multi class system, to make them stronger and there is a stronger class that requires special conditions. The game also introduced the Pachisi board mini game which is my favourite mini game in any JRPG ever:
Very rewarding equipment as prizes as well.
You could collect medals and exchange them for powerful itens, those medals are hidden all over the world, there is a trick to help find them but i won't spoil it. The exploration aspect of the game is flawless, once you get the ship it almost becomes open world. Sadly the game is lacking in bosses, when there are, they are good challenge and epic, but there is only a few of them.
Vagrant Story, i beat it for the first time recently, honestly, if you want a deep and maybe even convoluted gameplay mechanics, this is the one. There is a lot of stats and systems and submenus to keep track on. Your criteria:
certain battles requiring certain builds
Fits perfectly here, if you don't have the right weapon at the right boss you do literally 0 damage, and it is often, specially if you're new to the game, you're going to get your ass kicked hard, it's the hardest JRPG i've played so far. This game is just so unique it's kinda of a masterpiece, the enemy encounter is the best i've seen in a JRPG, every encounter feels like a deliberately placed challenge, which is the very much opposite of the vast majority of RPGs(J or not) encounters where the encounters feels like it's there just to waste your time. The Bosses are fantastic too, very challenging and memorable, each requiring specific ways to defeat it. The game have a very robust crafting system as well that unfortunately does not make any sense, like if you combine two daggers you get something so different that it feels super random, so a lot of trial and error is required there, just like fusing monsters in SMT 1 and 2. The game also have sometimes a out of place but fun and challenging box puzzles here and there. My finished save file say that i have explored 78% of the game, so there is a lot left there to explore and i heard there is a optional New Game+ super dungeon, with tough monsters and bosses.
Valkyrie Profile i haven't played much, but from what i did, it does fit the criteria, the gameplay mechanics can be pretty overwhelming at first, kinda like Vagrant Story, with lots of submenus and stats, lot of the content feels optional, and the game has 3 different endings, unfortunately the "good" ending is pretty much impossible without a guide, but if this "good" ending is like the "good" endings in others JRPGs, where everything is fixed and everyone is happy, then it might not be worth bothering with it.
Same with Chrono Cross, lots of optional characters, endings, content and exploration. And a crafting system.
Three others games that i haven't played it yet but i heard they are all about side quests and nonlinearity: Metal Max, Legend of Mana and Arc The Lad 3.
