@Monster World RPG: First, thanks a lot for the detailed answer. But before I cover it a few things I spotted in between.

Bug: On route to Sanctuary Stream, after beating the Chest mimic next to the star blocks, the treasure chest to its left opens by itself. But you still have to check the chest to actually get its contents (some Life Drops).

Bug: I got the Spirit crest from Aegis Sanctuary and did the first time trance. After that I collected the remaining 3 crests (+ 1 along the Legendary Equipment) and only then did the next trances one after another. But after the 4th trance (where Biomeka got shot into space) when I got back to the oracle, the Wind crest lost its color again and the two spots above it were still empty.
After the cutscene at the queen I could use the 5th crest normally to go to heaven, so nothing was broken beyond repair.

Suggestion: As far as I can tell, only the Monster Lairs have a rainbow over the entrance, if you did not get the item the boss left behind. I would really appreciate if every dungeon entrance had that too, if you're missing at least one hidden door or gold spot in there ("dungeon" as in going by the list in the genie's warp menu). Reason being that dungeons tend to be too long for my liking to check them all again from beginning to end.

Now to your answer. You mentioned quite a few things that bothered me because they simply were that way in the original game(s). I guess that's fine but I told you in my very first post that I never played those and am therefore judging your game completely as a standalone. I know that nostalgia is an important factor in fan games (I love all those references in the Hyrule Warriors games for example) but to players unfamiliar with the original some of those things might just seem strange.
In my opinion that should justify checking for each reference if it's really necessary to be copied to the point just for the sake of that specific reference. But if you decide against that (as it seems) I won't waste time and words to convince you otherwise. But maybe you'll keep this in mind for future projects.



Ok, that was quite a lot again! More actual game review some next time.