I know people asked before for the map to be changed. Since there isn't a key or anything, if we move our mouse over the icon, can a small description show up at the bottom of the screen explaining it? The other option would be having the text next to the icon, but that might get annoying if you're just moving it normally, looking around (like you do the majority of the time) and a wall of text shows up and blocks some of your view. Silent Hill had a map like Aquaria's, but the symbols made sense to the player when he looked at the map, so no key was required. Because as of right now, most of the icons only mean something to Naija, and not to the player. Lastly, someone said that adding notes yourself would help. I would like it so I could note where there's a secret I needed to come back to later. Since your maps are large, and the world is huge, this would help. Implementing it on the other hand I can see would be a pain. You have to make sure it doesn't mess with the other icons, and the fact that you have maps overlaying maps, the player would have to tell the game which one it's trying to select,... Also I do not understand why you get an icon on your map after killing a boss and not right when you meet it, but that's just nit-picking right now.
Having an option to play all the bosses again, either by revisiting the place again (that would be a long trek) or adding another option in the "MODS" section. "Shadow of the Colossus" and "God of War" (kinda) did this and it added to the replay value ALOT. The boss fights are soooo much fun to play. They are really the highlight of the game, for me.
Maybe when beating them you get a little message saying "new content unlocked" and you can then access it from the "MODS" menu. I know there's more to it such as which songs to give the person, how much lifebar and/or item/pets, etc. I don't know if letting the player decide via some options would be the best idea or presetting it. Presetting it (maybe with a timer) would give a "Challenge of the Gods" feel for those who really like this game and want a challenge in playing it, but giving options will let people play it either on easy or by stripping everything themselves, a "fight to the death" feel. Depends on which type of gamers you want to cater to.
On that note of "New content unlocked" could you add some of the key the cutscenes (story + memories) that the player goes through to the "MODS" menu? In the scenes you made Naija transform back to her original form so you won't have to customly re-record it for each game (some games have this problem when you enter an area with let's say a rocket launcher, and the cut scene shows them having a pistol. Such an old issue yet it still pops up all the time). After not playing the game for 2 weeks or so I really forgot where I was going and needed to look through the forums for help. I know some people said adding a journal or diary might work, but that seems like alot of work: making new content, adding it, etc. Maybe just referring to those cutscenes might be easier.
I know these are more than little changes, just my 2 cents. Good luck, thanks for the game.