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The permissions system was an issue with the CS5 installer. Unfortunately there is nothing you can do on that. The developers have noted this is an issue on the Mac side.
As far as the rest is concerned, they do this for a reason to make sure that you start fresh. This way if you had plugins running that prevent the application from running you can still run them in the older version while you await patches from other developers without having to risk your current installation. When you have programs that have so many plugins and extensions like Adobe programs it's actually a smarter way to do it. Also many will argue that you should use the same mentality when upgrading an operating system because you can run into incompatibilities with the upgrade that may not have happened if you backed up, started clean and then put things back on.
How was this missed on beta testing? What about neophyte users who find themselves stuck and having to figure this out via phone support to the far east?
Why can't extension manager handle these issues through a quarantine or add as you go method. Why isn't more of this handled with notifications during the installation?
OK, next problem. Where are the properties? I have same page open in CS4 and 5 and the properties panel is empty!
OK, how screwy is this! Properties panel is in place and not showing info. I go to menu and properties panel IS NOT CHECKED! Open properties window and it opens! So on the advise from this post, I had copied my preferences from CS4 to CS5 and this is the result. Beware... and be careful not to upset your workflow with this upgrade. Give it plenty of time to debug and repair.