Good idea, but there are easier ways to do this.
First of all, there is no need to reinstall Snow Leopard if you're already running on it. Just simply download Lion when it's out, and make a bootable USB out of it (you can find how to do this on the forums).
Boot from the Lion USB and erase your drive from there to do a clean install, if you want.
OS X cannot back up all of your Apps if you exclude the Library folders. That's where all the info is stored. For example, if you simply copy and paste the Photoshop folder in Applications from your old system to the new one, it won't run. It will be missing a ton of things in the user Library. Some apps don't rely on the Library, but those that come with an installer mostly do.
But if you're going to back up your Library folder, then there's not point in doing a clean install anyway, as that's where all the clutter is.
I would also not recommend excluding anything from the Time Machine backup. Who knows where some important stuff might be? Maybe you'll remember that you should have backed up System as that's where some of your fonts are, etc...
Just back up everything, and restore what you need. You can always not restore something, but once it's lost, it's gone forever!
I suggest installing Lion as an upgrade first, and then doing a clean install if necessary.