So here's my overdue review for this piece. I decided to look at the original to compare the changes you made to the 2012 original. And while I won't leave a review on it, I will drop a rating. I plan to review this piece almost as if this were a remix of the original. Let's start with the instrument choice.
I'll begin with the vocals. While the original's vocals sounded pretty good in the original, there were moments when they sounded a little 'fumbled', so to speak. That being said, the vocals here blow the original out of the water. They're cleaner and crisper than the original. In the original, around the 0:30 mark, there was this sequence that began and I immediately loved it. I was glad to see it in the original and I'm glad to see it here. It sounds really pleasing. The 'chimes' if you will, near the beginning, were a great touch to bring some more ambiance to the piece. Your medieval long drum sounds great. Personally, I enjoy when artists use unique instruments or define part of their style with unique instruments - I personally have been doing it myself. Everything else sounds nice too. No real complaints.
As for sound levels and mixing, your little sequence I mentioned earlier could benefit from a little sound boost. Just a touch. Maybe it's because I enjoyed it in the original and it was easier to hear there. Everything else is easy to hear and nothing gets too drowned out by anything else.
For composition, Mio seems slower paced than the original and that benefits the section greatly. Having a transitional phrase from Mio to Homura was a well needed addition. I enjoy how your piece pays tribute to your opponent you had. It's a nice touch. Optionally, you could have tried to 'mimic' Waterflame's style in Homura as so to contrast your tranquil composition in Mio to a recreation of Waterflame's style in Homura. While I think an idea like that would've given the song more symbolism, it's just a stylistic observation, not something that's a detriment to the piece. What's here works amazingly well. Homura maybe could've benefited from being slightly more intense to highlight the difference between Mio and Homura. All in all though, I'm enjoying what the piece is trying to do.
This is further reinforced by the song's theme. And while a song without an in depth theme isn't detrimental to the song, a song WITH a theme is ALWAYS a beneficial thing. I enjoy when a song takes its listener on a journey. It develops an emotional bond to the listener, allowing them to get more invested in the piece as a whole. I was emotionally invested in this piece because of the way it gently handles the listener and walks them through the piece. However, I think a final recap of the song's themes near the end would have been the perfect way to close the song. My personal interpretation of the song and its themes is a journey through life itself - complete with its ups and downs. Mio representing the tranquil moments (the 'good parts of life' so to speak) and Homura representing the more intense moments (the 'bad parts of life'). Under all of that, lays a deterministic drive to see everything through to the end, no matter how harsh.
This brings me to my final thoughts. Ambition is the fuel for innovation and innovation is the fire for success. Nothing is too ambitious of a project (Coming from a guy who wants to write and publish novels, compose music, get straight A's in university and still balance the rest of life) and nothing is 'impossible'. The original was hampered by some time constraints but this one utterly flourishes as a great piece. I have come to understand that you have gone through quite the large handful of hardships in your time but to press on and continue in spite of all that is commendable and this song is a testament of this. This 7 minute journey may have few flaws here and there, as all pieces do, but since it speaks to me on a deeper level than 95% of the audio on Newgrounds, I can't find a good enough reason to rate this below a 5/5. I commend your visions imbued into this piece. It's a drastic improvement on the original on all fronts and the definitive version of the Mio/Homura. If I have anything left to say it's the following: don't discredit and ignore your dreams. Even if others disagree, sometimes you must take your own path. And sometimes that path is a long, solo journey you must take by yourself. And something - something in this piece, reflects all of that. I wish you the best of luck on future endeavors.