There are always specific reasons why applications are removed and new ones are added from the default installation media; these programs are of course still available via the Software Center.
Pidgin replaced Empathy
Empathy is a GNOME Application and better integrates with the whole desktop environment. Before Empathy was developed like crazy Pidgin was the de-facto standard for most distros. Only when Empathy's development boosted, they replaced it. I don't see any chances of it being replaced any soon.
F-spot was replaced with Shotwell
F-Spot development was getting stagnant and there were hardly any active maintainers (IIRC). Right now there is only one major developer AFAIK - Ruben Vermeesh
On the other hand, Shotwell is lighter and more actively developed.
Gnome Shell replaced with Unity
Just a small correction. They are not replacing GNOME, but only the traditional gnome-panel which is anyway going to be deprecated in coming days. Means you won't get able to use it for very long. Later in a year or two you will have to choose between Unity or gnome-shell
Rhythmbox replaced by Banshee
Banshee has faster development as claimed by their developers. My personal experience is that their developers are usually very passionate about the software. I have met their developers on IRC and they are more than ready to help in case of any problems.
Just a good software is not a criteria. Active upstream development, active bug squashing, regular/predictable release schedule are the requirements.
Also Banshee developers tried getting Banshee on the default installation during UDS-N at Florida. This means they are taking up marketing and propagation too. I have always found them to be one of the best people in Free Software.
OpenOffice replaced by LibreOffice
I think every distro is planning to do so. OpenOffice is still under the clutches of Oracle and LibreOffice development is faster. There is no copyright assignment in LibreOffice as against OpenOffice.
You might want to know that always Ubuntu never shipped with pure OpenOffice but with Goo-org which contains many patches which Sun was not ready to accept in OpenOffice. Goo-org was maintained by Novell primarily. The application was just branded as OpenOffice but was Goo-org
PiTiVi was dropped
Poor reception and low rating in Software Center was cited as the major reason for dropping it. Secondly, it's target userbase was very small since it is a video editing application.
Banshee replaced by Rhythmbox
Space concerns were cited for dropping Banshee which had of late had suffered some regression in quality (controversial debate).
Tomboy, gBrainy and Mono Dropped
Since Banshee was the biggest user of mono stack, it was decided to drop Mono drop the CD itself and this Tomboy was also dropped. A game named gBrainy which also uses Mono was removed.
I can understand that there are confusions, but you cannot just throw an application in default and be sure that it's development is going to be still awesome till next release.
Every UDS you have a track called "Default selection track" where changes to default applications are discussed. They discuss which application's development is slowing down or getting buggier and the have to be replaced by which applications (if that is better)
My answer can have factual inaccuracies. Please point them out. I have written the answer to best of my knowledge and memory