For example: I come up with a system where basically I define 1 xml file which is then read by 3 different mechanisms to generate the m/v/c of a web application. the definition significantly saves times on web development when using the system.

Now look the argument is "oh its just a few algorithms used in a certain way, that should not be patented". however how is that any different than creating a ammo holder for .45mm bullets which can be put into any gun that can use .45mm bullets? Its just taking some metal and springs and putting them together in some novel way which has not yet been done before.

Remember once you see the invention that is TRULY innovative AND simple but nobody quite thought of using it that way before, it becomes a no-brainer. You start to think "yea given a few hrs I can make one of these myself without any special training or anything, without even looking at schematics, or even taking the one I have apart" but the fact is that nobody thought of it before.

The fact is, it was mentioned in a '96 letter, we must decide what part of programming is the "words" and what part is the "innovation" so that people can't do the equivalent of copyrighting words, but they can copyright books (the end product). (yes I am aware that patent != copyright, but try to see the analogy)