In my opinion IX is the epitome of the series, closely followed by VII and VI (and even though it isn't a FF, I would also add Chrono Cross in there without remorse). But with Final Fantasy it seems complicated to reach a consensus on which are the good ones, maybe because some people grew up playing that one or the other. And so, as biased as my opinion can be, I'd say that if you're in for the story those are the ones I would recommend checking out.

P.S: and as sanscript mentioned, Silver might be also worth a look.

My experience with Final Fantasy (and all JRPGs honestly) is that they have amazing worlds and music, but poor stories and combat.

The good old Manichean story lines. However, games like DQ7 and DQ11 try to camouflage the issue with many interesting twists and side stories.

Time for you to play some SaGa games; they are definitely not your typical JRPGs. SaGa Frontier and Romancing SaGa: Minstrel Song are both good.

Then again, the first part of DQ7 is rather unusual; before you even get to your first combat, you have to do some stuff in town, and then you have a dungeon filled with puzzles that feels a lot like a Zelda dungeon. Only after that dungeon do you *finally* get to see some combat (and that's following what I believe is the first mid-dungeon save point in the series, if you don't count mid-dungeon towns).

(I hear they shortened this in the 3DS version and they may have removed the puzzles; I have only played the PS1 version, so that's the version I am familiar with.)

Yes, the introduction has been shortened on the 3DS version.

There's also some other things I've heard about the 3DS version that are not at all positive. For example:
* Instead of random invisible encounters, there's visible encounters that move in real time, resulting in the game turning into an action game at times. To me, this is a major step backward, and would be my biggest single issue with this remake.
* For whatever reason, the class that requires Sage and Superstar/Luminary is not able to cast Multiheal in the 3DS version, even though, in the original, every character of that class would necessarily have that spell.
* It sounds like some of the balance tweaks done in DQ6 DS were applied here, and not all of them are that good. In particular, Vacuum did not need to be strengthened (it was already the sort of move that you would use all the time, in place of your normal attack, and at least in DQ6, making it even stronger put certain enemies (that use this skill) over the edge of fairness, I think). Meanwhile, Magic Burst's usefulness was already marginal at 3 * MP damage (especially since in DQ7 PS1 most players probably never learn that skill, as the only way to learn it is with one specific monster class that isn't easily accessible), and apparently it's now only 2 * MP, making it pointless. (DQ8 made it 2 * MP, but that was justified by the tension system, which could significantly boost it; that change makes no sense in DQ6 or DQ7. I note that neither DQ6 nor DQ7 has a full MP restore item (even though DQ5 did).)