So I finally have some time to fix up these levels. Honestly, I don't think there's all that much that needs changing on And So It Begins or Final Void at the moment.
The biggest changes are being made in Sanctuary Fortress right now. In the original, after the midpoint you had to backtrack through a portion of the first part of level, but there was a whole area to the right of the correct path that held a few extras and a yoshi coin that I think many people skipped going to in favor of returning to the start of the level to progress. This time, I've made the midpoint drop you off in such a way that you backtrack through the whole area, taking optional paths for the yoshi coin and powerups.
I'm also going back and trying my best to optimize the level because there are a lot of tiles in it. Sublevel 1B0 is going to be a pain to optimize though thanks to the weaving web of tiles partway up it:
It looks really cool but it's unoptimized as hell. I'll figure something out. I'm also thinking of changing the background completely because when I did it originally I just wanted to make the tiles from the backgrounds in Metroid Prime 2, not really thinking of whether or not it looks good. I'm thinking maybe I'll import the mountain background from Demon's Crest. I've gotten it working in Super Metroid before with great success; I can get it working here again. I just need to request map16 for it.
This is the Demon's Crest BG I was talking about.
If I don't go with that BG we'll have to find something else. One way or another, I want to scrap the BG.