This is a good point, actually. The changes I’ve made so far wouldn’t affect this - you’d still need to choose the folder afresh every time you moved to a new machine (but you would be allowed to do so). I’ve added a note to my development file to look at implementing this. One problem with have is Mac App Store support, where it’s not possible to store relative paths like this, because under the App Store’s sandboxed security system, the user has to have provided you with a full path in order for the app to have permission to access it. There are solutions for that, however (such as asking the user for permission if permission has not yet been given). So, I think this will be a workable solution.
~/Dropbox rather than /Users/homefolder/Dropbox
I disagree with that - I don’t think Ulysses is catching up (in the same way that we would never be able to “catch up” with them, either) because I don’t think the Soulmen are trying to do the same thing as us. The core features I built Scrivener for in the first place are not things Ulysses does or tries to do, although I can see they have made steps in the direction of some of them (images in the side bar, opening documents in different windows, multiple text view).
Scrivener automatically breaks up MMD files, but you can work around this by renaming the file so that its extension is something other than .markdown, .mmd or .md. If you change the extension to simply .txt, Scrivener will import it without interpreting it as MMD (and thus without splitting it up).
The next update of Scrivener will give it a more modern, polished UI. That is only a temporary stepping stone on the way to a much bigger overhaul that has already been in the works for two years, though, and which is probably going to take the best part of the rest of this year at least to finish. So, we’re not standing still, it’s just that some other companies have got their big overhauls out way ahead of us. 
Thanks and all the best,
Keith