You have no idea what you're talking about. The Java and Flash situations are totally different, with different ownership, licensing, and technical issues, and having nothing to do with each other. I'm not going to get into the issues with Java on the Mac, because it's irrelevant.
Apple normally updates only their own software on Macs. They do not have the ability, or in many cases legal rights, to reliably update third-party software. Any software that is internet-aware and thus may have wider security issues absolutely MUST have it's own updating facility in this day and age. The fact that Flash doesn't should be the real scandal here.
I'd also like to point out that the vulnerability addressed in that upgrade may be a moot point anyway. It has to do with flash content embedded in PDFs--the default PDF reader in OS X, Preview, ignores this bogus content (because it's brand-new, and nobody has ever used it except for transmitting viruses). If you're using something else, like, say, a full version of Acrobat, then you either have the necessary updates in there already courtesy of Adobe, or you have nobody to blame but yourself.