Some numbers on self-contained deployment. Currently, paint.net's installer (version 4.2.16) weights 12.2 MB, and once installed on a 64-bit machine it takes 111 MB of disk space (including a 56 MB Staging directory, but not counting the .NET Framework, which is shared with many other applications). The self-contained portable version package is 77.7 MB (more than six times the current installer) and, when uncompressed, it takes 192 MB of disk space, which, with the corresponding Stagging directory (assuming it takes the same as the portable archive itself, which I believe is a reasonable assumption) would go up to about 270 MB (two and a half times the current version).
Also, installing a private copy of the .NET Framework would negate any bug and security fixes deployed through Windows Update, which I think is a bid disadvantage.
All of this just because a small percentage of users are having problems with broken system libraries (which can be fixed with many available tools: System File Checker, the .NET Framework installer, even System Restore).
Offering a portable or self-contained version is useful in itself. It helps people with those problems, and allows you to test a new version without going through the full setup process (which is even more interesting in the case of pre-release versions!). But I don't think there is need to make it the default option. IMHO, it would be a lot better to just offer both options at download time: traditional installer and self-contained/portable version. That way, we could save *a lot*, both on your bandwidth usage and our disk occupation!
That said, I like it very much to be able to test a pre-release version without touching my working installation. Since I depend on paint.net for my workflow, in the 16 years I've been using paint.net I have never tried to install an alpha or beta version. But this is the first time that have dared, because it didn't involve any risk. That's very good!
Edit: I tried to post this in the build 7894 thread, which introduced the self-contained deployment, but it got closed while I was writing. Hope I have posted to the right place!