Excellent article/commentary! However, I'd add on this particular point:
A native Mac interface (no fancy UI)
This is just a preference for me, I want a Mac application to look like a Mac application. I donít want a custom colored UI or to emulate a notebook paper sheet.
I never got why people do that. I think it is another example of programmers deciding what is good for me instead of me. One ounce of flexibility is worth ten pounds of UI fanciness.
What I'd add or modify is the fact that Omni hides its beauty (or fanciness) inside until you get to know the application. Once you get to know the app, the things start looking logically simple and beautiful. Omni GUI is not a fad nor it tends to run for the title of the design of the day (like some apps that provoke one-time WOW and then the questions of usability and functionality keep popping up). There are two Mac software companies that I personally rank the highest for their consistency in producing highly attractive and quality-packed software: Omni and Panic. These rarely (if ever) disappoint.
One thing about OF that you haven't mentioned and that OF's current competition is missing -- underneath its surface OF hides lots of customization of styles (customize colors, fonts, indents, customize subtasks in the same way, customize the display of the left panel, etc.). Now, try to do the same with the competing products that supposedly offer a fancier GUI and you won't get far. Not to mention (as you already said) that some of competition is missing critical stuff such as sub-tasking or parallel and sequential arrangements. Overall, to me it seems that OF is a pro package suitable for biz, education, science, and home, while others are more geared toward a typical home to-do lists.
Anyways, excellent article!