I'm wondering that too.. I have used the software center (or whatever they are calling it) for quite a while and it never gave any errors like that. Once, a program didn't install right and left apt running constantly, had to kill it and run something (which I've forgotten) to resolve that (fix broken packages or something).
Though, installing via .deb files is pretty easy by itself (though, I don't think it resolves dependency issues). Not to mention, half the fun of the software stores is the browsing