On the other hand there is an inherent lack of system security features that can be applied to this approach, such as strict checksums and signature checking, and the packages do not integrate well with the system. Some of the benefit of shared libraries and other deduplication features of modern package managers is lost with this less integrated approach. Strict control over all installed programs is also sacrificed.
Was kind of thinking similar as well as far as security goes. One of Linux's "safety-nets" to malware is that the majority of software a user would get would be from the respective repository.. not 100% of course but would guess the overwhelming majority. "Portable" programs like these are convenient, but I could easily picture (just as an example) tricking gullible users into installing things, say finding a torrent for Half Life 3 beta or Microsoft Office for Linux. You know it's fake, I know its fake, random clueless guy who decided to try Linux because he saw Steam was available might not, and being a self-contained portable app with no fear of missing dependencies just makes it that much easier. Click click done, infected with a lovely rootkit or popup ads.
Also curious as to relative bloat.. some dependencies can be rather large depending on the program. It can be heavy enough mixing up say GTK and QT stuff, but multiple copies/versions for the various programs? That could get potentially rather fat. WinSxS and the GAC has a similar problem.. absurdly handy, especially if you were around for the 9x days, and at the same time it can get rather piggish with enough programs installed.
I also get what you're saying about possibly not integrating well too. Portable programs work rather well with Windows as you have a known set of APIs that's available and can easily have your program "fit in".. extremely unlikely you'll find somebody running a different shell than Explorer for example. With Linux you have an absurd number of possibilities to deal with that can potentially cause whatever program to either run perfectly or explode on startup.
On the plus side though it would solve a couple problems too dealing with dependency issues/conflicts.. dependency hell isn't specific to old versions of Windows and can be a pain in the butt depending on the distro.
I can see Canonical's reasoning more or less.. personally I'd be ok with it as long as it's "in addition to" and not "instead of" their existing package management. There if you want/need it, but won't get in your face if you don't.. think something like Chakra's bundle system. One click self-contained installer for "out of repository" programs that doesn't pollute the file system but it's not a replacement of their standard repos.