SD3 (fan-subbed rom, not the janky remaster) was such a vast improvement in gameplay and story flow but Secret of Mana was pretty great. Outside of that portion in the mid to late game where they do that stupid 'Sage isnt here go visit this mana temple' 'sorry sage still isn't here go visit this other mana temple' like 4 times.
It's weird, first time I played Seiken Densetsu 3 (in 2014) I actually didn't like it at all, was a big letdown after the like 15 years of hype. The controls felt a lot stiffer than Secret of Mana. I liked SoM's loose gameplay. ...which was too loose at times to the point that the game could be broken without much work (like spamming the Dark Force spell). Also thought SoM had more standout tracks. SD3 improved in pretty much every other category though. I replayed it in 2019 and appreciated it a lot more.
Probably not telling Gavin anything he doesn't already know, but SoM's mid-to-late game was heavily edited from the original storyboard. Game was supposed to be an early CD-based game called Maru Island, possibly Square's debut on the Nintendo Playstation. When the CD deal fell apart, a lot of the stuff they created for Maru Island got scrapped (and later reused in Chrono Trigger, which is why so many things in Chrono Trigger look just like things in Secret of Mana). Then they took what was left and made it Seiken Densetsu 2 / SoM, then that had even more of an axe taken to it late in development, losing a bunch of the second half.
The first 30% or so of SoM's world is likely pretty intact (just missing a lot of story and character development, like who the hell Thanatos is, or any of the other villains, as the others all appear out of nowhere late in the game) and then it gradually breaks down. The second half is a mess. I've seen it reported that as much as half of the game was actually removed during development. Not sure if this means half the game was removed from the time it was Maru Island / CD-based, or if it means half the game was removed from the time actual work began on SD2/SoM's SNES version. Either is pretty believable.
In any case, all those lategame palaces were gutted, and your characters just sorta get railroaded around to all of them quickly by some old guy on a mountain. Seiken Densetsu 3 reused the elemental palaces concept and actually fleshed out the story / world around them. So I think SD3 is a more complete version of an uncut SoM. And CT is SoM's genetic twin that contains a lot of SoM's early concept DNA. So between CT and SD3 I think you could find all of Maru Island's missing content and put it all together on a theoretical drawing board. Suffice to say, if it was gonna be some combination of Chrono Trigger, Secret of Mana, and SD3, then Maru Island would have been a pretty incredible game. So in some alternate universe there was a Nintendo Playstation and we'd be wistfully remembering Maru Island instead of Secret of Mana. Hopefully we also still got CT.
Side note: I know people who insist on referring to SD3 as "Trials of Mana" now even if they're talking about playing it in the 90's on a ROM. It's annoying. That's the name of the remake and the re-release that dropped a couple years ago, but it didn't have that name in the 90's. I guess rewriting history is becoming in vogue. Well either way this is a really minor thing to be annoyed about.