2. I hate having 2 "home" screens. I don't know if all of the skins have them or not, but I find it really annoying when backing out or hitting the home key and I get taken to the "wrong" home screen. It is a minor annoyance, but one that should not even be there.
Yep, this annoys me too.
The simple solution is to find the basic home xml file in the skin directory of your choice and replace its contents with those of the home xml file. This way, if you accidentally call the basic home screen, then all you will see is the standard home screen and it will be seamless to the end user.
Just remember that any SVN's may revert that change if work has been done in the basic home screen.
As for disabling modules, I'm not sure if this is what you mean, but in the plug ins section of configuration you can disable any of that main plugins (MyTV etc) by right clicking and choosing disable.
Cheers,
Marcus.