The first part is decidedly odd. If the checkbox is disabled, that means you don't have any list, so it needs to download the list. Unless your internet connection is denying it, this download should work (it works for me). You can try to retrieve it from http://saturn.installshield.com/ISRe...Downloader.ini and place it next to ISRedistDownloader.exe in the InstallShield System folder, although if it can't download the list, it may well not be able to download any redistributables.
As far as including multiple versions of .NET, we don't have a good story for that yet. I would suggest what you're doing now - make one or both into prerequisites and deploy them that way. InstallShield 12 has several prerequisite enhancements which increase your control in such a scenario, but if you don't have strict behavior requirements, 11.5 will do the job.
At this point our plan is to retire the separate .NET downloader support and implement it with prerequisites, but that's still a little ways off.
Michael Urman - Staff Software Engineer - Flexera Software: InstallShield Team