Definitely a number of changes going on here. The colors of the notes have been changed slightly, and the moveable bars (the one that plays the song, for example) also have went through minor modifications. I think the biggest modification that I have seen so far is the instruments section:
As you can see, the entire section to the right is what the waves of the instruments actually look like. Seems useful to more distinctly classify the sounds, but I myself can't interpret what they mean. Besides that, more percussion has been added and most of it has been re-arranged. The order I have the percussion set up in the screenshot is the standard Cave Story percussion for modding. The new order is Bass04, Snare03, HiClose02*, HiOpen02*, Tom03, Per01**.
Keyboard shortcuts have thrown me off so far. I'm used to using Ctrl+F1 for Song Settings, but now that's F2. And wowie look at that, the middle and bottom rows of the keyboard now function as actually using the piano on the left side of the screen. Awesome.
The song settings is mostly the same, but now it lists BPM to show what it equals to in Wait time.
There seem to be a lot more volume features this time around (there are two more tabs at the top to demonstrate this). It looks like they're mostly for easy fade-outs for notes.
I want to keep trying out more new stuff, but the obvious fact that it's in Japanese is preventing me from getting too deep into it. However, I am very curious about this "export function in a standard MIDI format" feature. Sounds extremely handy. I do hope a translation will come around eventually.
EDIT: The export MIDI feature is really awesome, and it blows the stand-alone program (on the Tribute Site) out of the water. I recommend trying it if you need to (Ctrl+Alt+M for easy access). Just note that for some reason the exported MIDI went extremely fast for me unless I set the wait time very very high. Something like 1500.
*The end of the instrument name gets cut off for me, but they are both the second ones listed.
**This is the same Per01 instrument as in the previous version, so it still won't sound the same in Cave Story.