If you're using a command line to initiate the install you can simply add /q to the msiexec command to cause a silent install (note that the video driver hook will cause the screen to flash a few times, which might confuse users if you're running it remotely when they are logged in).
the install of 3.x does not uninstall 2.1 or 2.2 so that will have to be done manually. I've been able to install multiple versions at the same time too.
Lastly, the settings. When I created an MSI and MST for this I found out which registry keys controlled the settings. I edited it so that it used NT security and added a group of users to the list of people allowed to remote on to the machine. I also changed it so the user was prompted to accept the connection with an autodenial timeout of 10 seconds.
This was a bit tricky as the security group corresponds to a load of binary data in the registry so you have to be careful to get it right, but it's only one or two keys so not much work once you know what is changing.
I'd suggest using procmon to monitor the regitry changes as you make the necessary changes to the settings and then add the keys to the MSI using an MST file.
there may be an easier way than this, but i'm not aware of it.