Updating your Android device and having the latest stable version is always a good thing to do and its really recommended when you upgrade versions (4.0.4 to 4.1 for example). The only downside is that some stock ROMs bring a preinstaller apk that will not only install some random junk (depending on the country of origin of the ROM), it will also install it in /system so you can't uninstall it.
This might seem a downside when updating our Android device, but knowing how to create our own update packages, when can create a script that will delete the apk before it installs all the bloatware. With some little tools, we could be able to know what's packaged inside the ROM and create our script to clean all the bloatware we want. The tricky part is that once the stock ROM is flashed, we need to restart the phone in recovery mode before it restarts in normal mode. If the phone restarts normally, it will execute the preinstaller apk.
In Samsung Galaxy's case, we can extract the stock ROM file and open it via DiskInternals to see what apks are present and know the names of the ones we want to delete. Just remember to delete PreloadInstaller.apk and PreloadInstaller.odex