Right. Lunaris, your post is a veritable wall of text
Which explains the broken quotes, actually - it's to make the posts less larger when quoted. (Nested quotes, in other words, are disabled.)
Ooh, okay.
I just numbered the replied parts in your post, rather than quoting it individually.
Maybe. Maybe not. I don't know just yet. Though, a bonus boss would be utterly brutal in the Tower, if I were to add one. Will I add one? Perhaps. Perhaps not. All I know is... if it is going to have one, it will possibly be an NPC that you have encountered in the past. 
Sycor? :3
While I was considering making each outfit a decorative thing, perhaps having them grant useful abilities could be helpful.
That's be interesting

I'll get to work immediately and post it here as soon as possible. (And at the Cave Story forums as a status update, probably.)
Cool~

Serenity wearing some kind of school uniform. Not exactly sure what kind of school uniform that actually is, as Yes Town's school uniform is much different.
School uniforms? Noooo D:

Serenity cosplaying as Kalifa from One Piece. I found it ridiculously hard to sprite the glasses, strangely. So, I left them out. (Besides, Serenity can see perfectly well without glasses, and if she were to wear glasses she'd risk ruining her eyesight.) This outfit will definitely be hidden in the Top Floor area, and can only be obtained after you can reach the Master's Room - sometime before you battle Shinica and Luna, though.
Wait, so fishnets are actually going to make an appearance of sort?

And yes, Sycor has the castle emblem (a moon).
The castle emblem is a moon. It was always a moon. IT WILL ALWAYS BE A MOON!
... which is actually meaningful considering the master is technically a lunatic. 
Can I ask what you mean?
Here's draft #1 of the Sunset version of the Tower area.
Draft #2 will be coming soon! I hope.

Looks okay.

Draft #2:

Looks better than okay.

Say, you wanted to figure out what tileset you could use for the Top Floor, right? Why not the original Cave Story's Sacred Grounds tileset?