Like you, one of the things that really drew me to the MMD format was its “future-proof” format. Plain text with open source standard parsing engines. You really cannot go wrong with that combination.
As for Scrivener vs. a text editor: It definitely comes down to document size, in my opinion. There are plenty of MMD files that I create that never go in Scrivener, because they are small documents with simple organisation. But a large project, say a book, will be greatly served by an organisational application such as Scrivener, which can export to MMD plain format for archival once the project is complete. Besides keeping track of plot points and section status, the matter of document structure is made much easier with Scrivener as well, since it automatically generates headers when you compile. It is possible to adjust section order, create chapters, move chapters between parts of the book and so on—and all of the ‘#’ syntax will be taken care of for you.
Even with a project as “small” as an article can benefit from this sort of treatment. A user working in Scrivener with the intent of producing MMD documents can either choose to ignore all of the formatting features supplied, or they can use them as a form of meta-data that will be ignored upon export. Granted, some features simply do not work, such as list generation and tables. These will produce unreliable results in MMD, and standard plain-text methods are preferred.
Another advantage for individuals with a lot of figures is Scrivener’s ability to keep resources all together. You can link to images by dropping the file into the appropriate portion of the image syntax, and Scrivener will not only create the path for you upon export, but it will dump all referenced images into a convenient directory with the MMD file. This way you can avoid long absolute paths in your source document.
There are certain areas where a tuned text editor (such as TextMate with the MMD bundle installed) will make editing MMD files much simpler from a syntax standpoint, so it really comes down to, as said initially, the size of the project. Larger projects that will benefit from organisation can take a hit on the syntax level—but for smaller projects it is simply easier to use TextMate with all of its syntax aids and colouring. Another option here is to set up your system (a bit more tricky with Leopard, but still possible) to allow TextMate to interface with Scrivener as an external editor.
But in general, I feel the two compliment each other beautifully. Scrivener is by far the most beautiful interface I have encountered for large scale projects, and MMD is by far the most stable format in terms of longevity and flexibility. I find that for the most part, the lack of syntax colouring and so forth is mitigated by Scrivener’s interface—and frankly in an average project you don’t run across that much pure syntax. In a small help document, sure, but in something like a book—for the vast majority of the time you’ll just be typing like ordinary.