I started out on Final Fantasy. I never questioned its methods. In fact, when I started branching out in to games like Baldur's Gate and Final Fantasy IX, I found that the inability for everyone to learn every ability and absolutely max out their stats to be a bit strange and even decried it as bad design.
Years later, after damn near exclusivity to WRPGs, I have revisited games like Final Fantasy VI, VII, VIII, even, X, and Dragon Quest...whatever... and found that the party were ultimately homogenous; everybody could have access to max stats and all spells and techniques after a sh*t-load of grinding. Since you could do it in one playthrough thanks to an infinite supply of XP, AP, PP, what-have-you-P thanks to random encounters, this begs the question:
What is the dayum point of having different party members when they're all the same?
In FFVI, everyone could learn magic, which had the highest damage-dealing potential of all moves (in theory). I just had one party who I maxed out and didn't use the rest.
In FFVII, I just switched my Materia around whenever the plot called for a particular party member, but I always stuck with Cloud, and the others (I don't freaking remember)
IN FFVIII, I just switched my Junction setups around whenever the plot called for me not to have Squall, Selphie, and Irvine.
In FFX, you could max everyone's stats through careful manipulation of the Sphere Grid. And even without exploitation, you could have everyone know each skill, and build their weapons to address their weak points.
In FFXII, every character could learn every spell, technique, and gain the ability to wear any piece of equipment. Rendered moot because you could rely on Quickenings for DPS in the end.
By the end of these games, nothing really differentiated the party members except for their Limit Breaks/Overdrives/Whatever, and you couldn't rely on them except for 6 and 8.
And we look upon those games as paragons of design. The best design is one that actually uses the skills you've given your actors that allow them to PLAY A ROLE in combat (or, ideally, the rest of the gameplay, too).
Anyway, thoughts?
FF6: Everyone can learn magic, not everyone is effective with it. It takes very careful management of your level ups to make everyone highly effective with it. On top of which, Gogo becomes super overpowered just by mimic alone. There's also Bum Rush, Quadra Slice, learning X-Attack while having a Genji Glove on... It depends on how you WANT to play. If all you did was jack everything you had into magic and didn't look to see that everyone else becomes super OP as well, then you're honestly playing the game wrong, or only played it once. On my first playthrough I used Locke and Celes almost exclusively in every party and switched out the other two members depending on what I was doing. Sometimes, I'd carry Gau as some of his Rages were quite OP and/or useful, sometimes I'd carry Setzer... It just depended on what I was doing. FF6 is designed in such a way that no matter WHO you want to carry with you as characters, they all become super OP by the end of the game. Whether that damage is dealt through physical or magical. A lot of their abilities even make them VERY FAR from "interchangeable", if you're using them properly.
FF7: I'd comment, but I don't care. I personally thought the game was a massive travesty in every possible way imaginable. I got two hours in, shut it off, never looked back.
FF8: Yet another FF game I thought was completely ******ed. Yeah, I totally want to play as a cracked out Emo Kid with all the personality of a rock. Without likable characters, I couldn't enjoy any aspect of that game.
FF10: I enjoyed this game for the uniqueness of each character (if you didn't notice it, you either didn't play the game, or have no clue what you're talking about). The only real "unique" trait that could be passed to others is "Piercing" on weapons. Which, all that means is, everyone can hit and kill armored enemies instead of just Auron or Kimahri. I suppose you could say anyone could learn to be a healer or a magic user... But only Yuna can summon and Lulu becomes a massive powerhouse once you drag her into either Tidus's or Aurons sphere grid. The major complaint I have with your analysis of FF10 and "you can make everyone the same!" argument is the sheer amount of time and willpower you would need to DO that. I, for one, refuse to invest THAT much time into the game to do it. By the time I had to fight Sin when he was flying, everyone was at the end of their particular grid and had to break into the next one. Know how many hours that was? 80! I'm sorry, but I'm not going to grind to max everyone out, and I doubt many other players will either. We're going to take one, maybe two grids for each person, and beat the game before getting too much farther. You don't even need the optional content to beat the game, so you can ignore it all. Celestial weapons? Ignore 'em. Capturing monsters to build stronger monsters or rare items? Don't need them. Sure, at some point, you can make everyone the same, but why would you WANT to? The massive time investment alone is a good reason to specialize characters and leave them that way. On top of all of this, we still have faster monsters more easily killed by Tidus, flying monsters more easily killed by Wakka, machines more easily killed by Rikku, and armored enemies more easily killed by Auron (especially since his attack power is far higher than Kimahri's is for a massive chunk of the game).
FF12: Yeah, everyone can learn everything. Again, this takes a long time. I invested something like 95 hours into the game before giving up, 'cause I wasn't even sure I was at the HALFWAY point of the game yet, and was still using spells like "Fira". I hadn't even seen level 5 magic in any school yet for purchase. Honestly, it was far easier to specialize the characters I liked, and keep those ones with me. I turned Fran into my resident Summoner/Black Mage. I gave her every single Summon and gave her every single attack spell. I also specialized her in staves and cloth and such. It wasn't a system I enjoyed that much... But, at least it gave me the freedom to choose what I wanted my characters to do right from the beginning, and then do what I liked. I could carry characters I enjoyed with me, and ignore those I thought were stupid or boring. Which, really, lead me to leave Penelo and Vaan behind almost 99% of the time.
Basically, I don't understand what the complaint is. I, for one, hate specialized characters in an RPG. Why? It leads to "the holy trinity" of RPGs. Tank, DPS, Healer. Everyone will bring THOSE particular characters along with them in EVERY RPG that limits and specializes characters as an effort to "make them unique" from each other or "make combat worthwhile". Of course, game developers are doing this wrong, but how would they know when everyone buys these games regardless of how poorly managed a combat system is? Especially when RPG fans so irritatingly tell you that "a good story can make up for terrible gameplay". Well, if that's the case, just read a book, same experience. A game needs a good story, yes. But a game also needs good gameplay, because you'll be interacting with that for almost 90% of the game as you move from story segment to story segment.
If you create characters that have "specializations" or "unique abilities" in combat, but leave it so that the player can also CUSTOMIZE these characters as a means of either shoring up their weaknesses or using them in ways the designers hadn't anticipated, this is somewhat more fun. The player feels they have more control over combat as well as the freedom to use WHOMEVER they want, instead of just the token characters that form the Trinity. This allows for more diverse parties across players and even playthroughs. It means that not everyone will take the same characters. People will pick who they enjoy instead. Going back to my FF6 example for a second, it's what I did in that game. I turned Celes into a physical powerhouse and never really used her magic. I gave her an Atma Weapon and some of the best gear, and she became my main DPS and tank in the game. I carried Locke around with me for the sole reason of stealing anything that wasn't nailed down, as well as because he was my favorite character in that game. I never really carried Terra with me all that often 'cause she bored me to tears with her arc, and I didn't carry Sabin along with me 'cause I thought he was rather boring as well. I turned Edgar into a magic user and never really touched his Tools other than "Chainsaw" most of the time. I more often than not would end up with Setzer in my party and Mog or Cyan. I played with the characters I liked, and relegated everyone else to benchwarmers, only leveling them up enough to take on the bosses at the end. I was able to do this, 'cause the Magicite let you customize your characters. I guess I COULD have found them all "interchangeable", except that the measure of "interchangeable" shouldn't be roles in battle, but roles in the story. If characters can be interchangeable in battle, then players are more likely to pick who they enjoy, rather than who is most effective in combat. The only real issue with "interchangeable" skills and abilities in combat is how dull this makes combat because of how combat is often designed.
Combat, itself, should be more varied and versatile than Any Final Fantasy Game ever tried to be. Some characters should have advantages against some monsters and disadvantages against others. Some characters should learn skills or abilities that are more highly effective against other monsters. Characters should also be unique in that some monsters just don't hurt them that much. Pokémon is a great example of how this works and can be effectively executed. Unless you're min/maxing in that game, there's little reason to take "the very best mons" with you anywhere. Take what you enjoy, it's all effective enough to beat the main storyline of the game and stay in your party until level 100. None of the Pokémon are really that "specialized" that they can't fill two or three roles in your party at once. Other RPGs don't do this, and their combat is somewhat lacking. Most RPGs combat boils down to "weak to magic" and "weak to physical hits". Some try to spice that up by going "weak to fire magic" and "weak to ice magic" while never really doing the same to the physical side of the spectrum. It's one of the main reasons EVERYONE takes a magic spell caster with them in every single RPG. Combat is designed REALLY poorly. It's designed so poorly that what WEAPONS and EQUIPMENT you're using rarely matters unless it's just "too weak" for the monsters you're fighting. The difference between a whip and a flail in terms of the game's combat system is 10 points of attack power. Not helpful, not useful, not making combat interesting or fun.
Anyway, that's my two cents.