I don't understand why HTC would do that.. It's a huge inconvenience. I love Sense, but I like my other launchers more, because they're so much more customizable than Sense itself :/
If you want the clock then get Beautiful Widgets (I used Beautiful Widgets before I got my inspire, its a nice app and looks pretty much identical to the sense clock, but is customizable like crazy).
Im not sure about a specific favorites app, but I am sure there are plenty.