Mike,
First, the installer only adds the program group if you tell it you want it to. It’s on one of the configuration pages you step through when you install MyEclipse. The default is to create the program group as this is the expected behavior with double-click installers. Adding the group make it much easier for more novice users to conveniently launch Eclipse, rather than have to mess with creating their own aliases manually.
Keeping a separate workspace directory is not a problem at all. If you like the convenience of the program group, simply edit the alias it points to and add your -data option and you’ll be all set. Personally, this is exactly what I do. On the other hand, if you don’t like the program group, simply don’t select it the next time you upgrade MyEclipse. No problem either way.
–Scott
MyEclipse Support