A Japanese magazine featured this Secret of Mana world map before the game was released. Clyde Mandelin of Legends of Localization was too kind to scan this map for me:
Wow! What a difference. Before we get excited about potential lost content, let's consider some caveats:
1)It could be a mockup --- they may have had an idea of where they were going, and decided to create a map to give a feel for the game.
2)It's incomplete --- the text in the lower right hand corner covers something, or they hadn't developed that part of the world yet.
3)The details of each location may be for illustration only --- just because we see landscape, doesn't mean it was the exact landscape intended
4)It's not clear --- it's hard to make out details on this page.
That being said, let's get to work. Let's flip the map, remove the text, and see how it's closer to the final game than it seems at first glance.
This is better, though many things are way off. Here's the final world map for comparison, courtesy fantasyanime.com:
It is impossible to make definitive conclusions about similar areas, so I want to be clear that none of the following is anything but speculation. This includes the possibility that I'm misidentifying locations. The Pure Land was moved in the final game; it looks like it's where it is as a placeholder. The shape of the volcano is almost identical.
This map more or less confirms my hypothesis from the first article that the overhead view of the world map was intended to be more detailed. Look at how many paths are defined even though it's a rough draft.
In the lower left corner, we see that beta Tasnica was a full kingdom. I'm going to assume this was Tasnica due to its location, and the castle being surrounded by water.
There's no isolation here, other than the Lofty Mountains. Also note that there is a structure to the right, which I imagine was one of the Mana Palaces, or other lost area. There are other locations in the vicinity that we can't make out. Speaking of the Lofty Mountains, they appear to be mostly the same, with an extra open area in the middle.
Let's look at Kakkara's area next:
This is a very early version of Kakkara, as hardly anything is present beyond the Moon Palace and what we can presume is the town itself. The Moon Palace's surroundings are essentially a black hole, but here it looks like it's smack in the middle of the desert. There is no detail in the landscape.
What I presume is the lighthouse is essentially in the same place with a bit more detail. This looks more like what you would expect:
There are two islands that don't resemble anything in the final game. I've moved them together in this shot:
The only small islands beside the Lighthouse's are Turtle Island and the Gold Isle, neither of which is represented here. There are some other islands with no content that also have no correlation.
Onto the Ice Country's full continent. Remember this area from the final game?
Maybe I was wrong about the clearing on the left being a port. It could just be the remnants of the beta continent:
Notice how the ice portion slowly merges into the area on the right. There is some similarity between this and Altena in Seiken Densetsu 3, seen at Fantasy Anime here.
Finally, the first area of the game, final and beta:
I had to flip things again to reconcile the two. The area inside the natural mountain wall is the only portion remaining. I have no idea what was lost to the north, but the Upper Land and Matango may be in here somewhere. Also notice how the Enchanted Forest in the final game's map is very similar to the same area in the beta map, neither of which represent the Enchanted Forest once we get there. Whatever the area is with the bridge and sand in the southern part is nonexistent in the final game. It also appears that there was no transporter present, and one could simply walk to the Enchanted Forest, or whatever it was intended to be.
The good news about the first area is that we have screenshots of the active view during development! Unseen64.net published this article about Secret of Mana pre-release in 2008.
They wondered about a square area bounded by a river, seen below. It's actually near the Water Palace; you can see this in the beta map above. The transporter near the Water Palace also seems to be missing in the beta map. I've appended a screenshot of where this is located in the final game, as well as what happens if you land there.
As far as Northtown with the road to nowhere,
I personally could not find a direct analogue on our early map. One of their screenshots shows an overhead view of the world with landmasses not in the early map, so there were already changes made by that point. As for beta Gaia's Navel...
...this is more or less how it is in the beta map above, with just one large river flowing down the mountain.
After our journey here, I'm quite sure that there was a working incomplete beta of the game which was used for promotional releases during development. The notion that the early game is more complete in the final version makes sense if this was the priority during the beta's development. It is unknown how much of the beta map was actually coded, and what parts were intended to be replaced anyhow It's possible some ideas made it into Chrono Trigger, but a cursory glance at those world maps does not reveal anything notable. When the CD-ROM addition for the SNES was cancelled, they didn't have to alter part of the game, they had to mostly start over.
In other news, I'm glad I got through an article without having to translate any Japanese.
Next: The Ballad of Purim and Dyluck
Acknowledgements: Once again, a huge thanks to Clyde Mandelin for scanning the Japanese magazine. Unseen64 allows their work to be used under this license. Square owns everything.