The Castle thread (spoilers on the past, present and future areas, as it's in one map).
The Corrupt Moon, the Hallow Sun. Two areas made both of machinery and magic.
Those two areas, though not accessible in Lunar Shadow, still play a vital part in Lunar Soul.
One of the areas in the Tower will let one change the position of the two areas. Either the "moon" will be near the Top Floor and the "sun" near the top part of the Tower, or the other way around.
Two bosses can only be battled when the moon is on their side of the castle, and a third boss becomes visible if the sun is on its side (otherwise it's invisible; it's minions are still visible though).
That boss will act like the (normal) Core from vanilla Cave Story.
This will also relate to the three endings I've planned~
Wow, you've planned some things in advance, huh?
I might already have one planned
Though, whether it's mind shattering or not, I don't know.
I'm not ready yet to state what the planned plot twist is, but I'll probably post it later. It will tie in with two of the three planned endings.
(It'll most likely be a wall of text.)
Cue the wild and possibly ridiculous guesses?
Though those could be good for a laugh or two.
You mentioned three endings, so I take it that "leaving the castle" doesn't count as one?