At least the first two problems are the exception not the rule.
I want most of my USB-Drives not to be used as a Time Machine, therefore it should be the rule: Drives are not used for Time Machine unless noted otherwise. Since there's a pref pane for it, it wouldn't even need an extra button.
Most user's will not prepare the layout of the files and folders in some fancy way, so just show them arbitrarily, unless otherwise noted. Just hide the option in the "Get Info" dialog.
Drive Indexing options could be hidden in the "Get Info" dialog, but I'd be fine with keeping it enabled by default.