This post may be a little premature, but I'd like to at least let everyone know that we hear your concerns and actively seek solutions to them.
Ron mentioned at the JSP 2008 conference that the Hot-Fixes for a particular version needing to be installed in addition to the full release version was a problem, in terms of resources.
Well, it looks like Hot-Fix #3 for 06.05.12 will be able to be offered as either a separate package to install on top of 06.05.12 (hot fix 1, 2 or none) AND as a 06.05.12 Hot-Fix #3 applied full install.
This means you can bring existing installations up to Hot-Fix #3 by simply installing the Hot-Fix #3 on top of 06.05.12 (as Hot-Fix #1 and #2 did) OR for complete new installs, you can install the complete 06.05.12 with Hot-Fix #3 already applied.
Like I said, this may be premature - we've built build #1 of Hot-Fix #3, but have not yet passed the full install of 06.05.12 with Hot-Fix #3 applied yet... barring any problems, it looks like we get to keep everyone happy with 06.05.12 Hot-Fix #3.
Oh, and yes - there will be a .MSI - so group policy deployments can make use of this