You seem really committed to this project, and that is great to see! You have already got a sturdy base to work off.

Magicant has a lot of potential to be used for exposition purposes, considering that it was born of Maria’s consciousness. In the same vein as Ness’s Magicant, it can be used to reveal information that Queen Mary has forgotten. Perhaps Ninten could find some clues as to the truth scattered around Magicant. This can also, perhaps, help give Ninten a genuine reason to seek out the Melodies.

The first three Melodies can be attributed to coincidences because they are obtained through random deeds of goodwill (stopping the poltergeist attack, returning to baby canary to Laura, dealing with the problem in the zoo), and it is after the first three that Ninten first visits Magicant in-game, at which point he could start actively hunting down the Melodies.

The MOTHER manual implies that Ana has been calling out to Ninten since the start of his adventure — you can incorporate this into his incentive, too.

As for the PSI learning process, I have always felt that MOTHER is the game where PSI is treated as the most traditionally mysterious. In MOTHER, the characters are not chosen ones, but just a small group trying to survive, a point that the futility of power near the end of the game drives in. I think that instead of separately bringing attention to every new ability Ninten or Ana learn — there are a lot — you could simply have them be used in battle without making it seem like much of a big deal.

For example, you do not need to divide Lifeup into “Lifeup Alpha”, “Lifeup Beta”, “Lifeup Omega” and so on, and have each of them commented on. Instead, you could simply treat it as “Lifeup”. Display their progress with Lifeup in how it gradually becomes stronger over time, and even gains the ability to heal multiple allies at once as they become better at it. This alone will lower the number of instances in which they develop new PSI abilities, and will also deal with strange mechanics such as Healing’s very selective effect depending on its levels.

After all, listing their PSI abilities with strict effects, PP cost and the like is a very scientific, clinical perspective — Ninten and Ana are twelve-year-olds, and are unlikely to closely scrutinize each ability. They are unlikely to analyze say, Lifeup beyond “this heals people” and PK Fire beyond “this burns stuff”.

They are similarly unlikely to say, “This is PK Thunder Alpha, which deals electrical damage, and this is PK Thunder Beta, because it deals more electrical damage than PK Thunder Alpha”. Instead, they are more likely to just realize that their PSI is getting stronger over time and use.

As an aside, it is not confirmed or implied in MOTHER that George specifically stole PSI information. Giygas just refers to it as “vital information” and makes no reference to PSI. All Encyclopedia MOTHER tells us on the matter is that George studies PSI at some point after returning to Earth.

It is, in fact, probably more likely that he stole alien technology, considering that George, who had not (as far as we know) particularly been known for his scientific ability, was able to create an underwater base and a robot like EVE.

Of course, this is just a clarification — George stealing PSI information is still a route you could take.

All in all, good luck with this project!