I downloaded the ISO yesterday and intended to install it today. However, reading through the early responses over at aw.net since then I've been a bit put off.
On top of the issues mentioned here, it seems a few other things don't work as expected. Some inbuilt shell commands don't behave as they should. For example
Set foo ""'
This assigns the empty string to local var $foo in earlier versions, but fails on 4.1U1
If ?
This displays the template for the 'If' keyword when entered in a shell in earlier versions, then fails (as it's only valid within a script), but apparently fails immediately in the update.
TBH, I really don't see what the WBStartup thing was about. One of the best things about the existing system was it's sheer simplicity. I can understand that perhaps people don't want to drag stuff there and forget where it came from if they ever wanted to put it back or disable it, but there are surely other ways to deal with that (tooltypes to mark as disabled and where a tool was dragged from might have sufficed, for example).
As for not running scripts, that's not good for me. I use a few ARexx scripts to extend my Workbench with various shortcuts that I've been using since OS3.5 and still use in 4.1.