Thanks everyone for the excellent feedback! A few additional questions:
1. How well does Mellel do with formatting end notes (if I can get by using end notes over footnotes so at least the formatting won't be all crazy)?
2. Between Mellel and Nisus Pro, which has better performance? When I've used Mellel, performance was pretty good over Word. I almost had the hang of exporting Mellel docs to Word with very few "conversion errors".
3. Are there any training videos on Mellel, or any other training besides the "big manual" that'd help me learn more quickly and easily (like a "Mellel for Dummies"?
4. What's Scrivener? I've faintly heard of it but never used it. Sounds interesting.
5. Any suggestions of storing research notes in Accordance User Tools? Good or bad idea? It'd be searchable in Accordance and a little less clunky than having to use Logos Personal Books and re-compile all the time.
6. Thoughts on Microsoft's new OneNote for Mac? I store all my college documents in OneDrive and all my company docs in SharePoint, so would this interface better with my workflow?
Re: 1. You won't have a problem. I had a 30 page course paper, in which I used footnotes. I wanted to edit this paper and submit to an annual conference, in which case I wanted to clearly see how many pages I needed to edit down. Mellel worked like a charm, with either footnotes or endnotes.
Re: 2. Depends on for what. Text manipulation? Charts? Graphs? Document length? Hebrew font rendering? Not sure what you mean by performance, as it is relative to a task.
Re: 3. Mellel has several tutorial videos. It's not that hard to learn—just start using it. Software learning is an empirical process! Just start using it, and solve each problem when you encounter it.
Re: 4. Scrivener is a research/writing application. If you are doing Hebrew, forget it exists. It's also heavily reliant on Ms Word or another editor. Also, it doesn't support Live Bibliography like Mellel does (which is very handy at times).
Re: 5. Funny. My advisor keeps all his notes on Qumran in Accordance. He is the Accordance note master! I like the idea, and have recently started to use them more. All of my data on my thesis is in notes and a tool.
Re: 6. Wouldn't have a clue. I detest MS Word and Microsoft products. I bought a Mac for a reason.