Why? The whole point of backing up is to back up everything because you never know when your drive is going to fail or what files may be inadvertently thrown out or overwritten. The beauty of Time Machine is that it makes backing up easier than not backing up.
Apple has thought of this, and developers can designate in their applications what file types and locations should be excluded. It is likely that someone will come up with a file wrapper that provides and interface for this.
As it is you can exclude specific files or folders.
I do not back up my Apps or System Files.
If you select your System directory to exclude, you get the option to exclude all "system" files. This makes it so that only data that is not in /System /Library or /Applications is backed up by Time Machine. I also have it excluding ~/Downloads and ~/Library. This is because I have a Macbook Pro and have it set up to operate off of the main disk and then use an rsync script to sync my backup to a colocated server that I have.