I think we can see this in like a huge amount of RPG franchises. It feels like every major RPG release that isn't a smartphone release seems to be getting longer outside of maybe Square's stuff.
In general, RPGs have focused on story more, PS4 exclusives are an example and there are good works. But most mediums these days, the quality of writing has dropped.
Story focus isn't the issue, it's the 'degression' of writing.
I haven't played SMTIV and A but I have heard mixed reviews on it. Older fans disliked the direction the game took, and newer fans liked it. From what I hear, the main reasons for the dislike, was the poor writing and that the story was dumbed down (I can't give a true opinion as I haven't played those games).
There are different variations of the storytelling, games that are action focus can still offer a good story. Soulsborne games for instance, the environment does the storytelling for you, absorbing players into a world. The old SMT games follow this approach too through NPC dialogues. I can see it being the case, as I am currently playing SMT 1.
I am not a fan of absurdly long video games, but a few exceptions can be made if the world exploration, writing and gameplay are top-tier...they come in a rare package.
Another factor is age, when we're younger we could invest more time in games but as we get older, time is scarce. Games that drag on too long ruins the pacing, and on many occasions, fillers ruin the experience.
Nier Automata is the longest title in its franchise but as a single game it has good optimum length, 60 hours avg completion. FE: 3 Houses garnered good reviews due to gameplay and story, which FE: Fates lacked so much of, and both games are roughly the same length.
Finally it's preference. Most current JRPGs follow the mainstream direction, to service fans with familiarity. The familiarity is anime. Anime itself isn't bad, but the hyperbolic of it is. It can strip away a franchise's image, core principles and identity.
If a JRPG from it's birth intended to be cliche, fan-servicey, at least it sticks to the core of it's identity. But with most JRPG franchises, they are radically changing themselves to desperately appeal to a specific audience (young people, otakus etc). When they don't get that their winning attributes was their own uniqueness.
Creators for current mediums, seem to generalise young people that they are "all into the same thing", which isn't entirely true. There is going to be a point that people will be sick of repetitive tropes, and demand originality. Many of us has grown out of cliches, simplicity. We want to see impactful works.
Rampant shifting and fanservice, results to messy storytelling. Another reason why FE: 3 Houses succeeded was because it deviated from that intensity, compared to Fates, which was overblown of it.
FE: Awakening had fanservice, but not bad as Fates (minus the dragon loli). The story of FE: Awakening was fantastic and 30-40 hours avg long.
So in summary, games do not need to be longer to make a story good. Quantity shouldn't be the emphasis, it's Quality.