Apart from getting automatic updates through apt-get upgrade and chain updates from library dependency upgrades, why would one use Ubuntu packages versus .deb files you could get from the software manufacturers? (e.g. Skype, Eclipse, Opera, etc..)
Could be any number of reasons, depends on the user and source.
My general advice is that if is in the repositories, you are going to be better off using the Ubuntu repositories.
If not, IMO, you are better off compiling from source. Implied in doing so is at least some cursory review of the code. yes it is unrealistic to expect end users be able to jump in and start reviewing source code, but nothing wrong with getting a start. You will pick up on major problems (the code will not compile) off the bat.
If the source code is not available, and all you have is a .deb it comes down to trust.