After releasing, Emon managed to suggest some things that would streamline the JK Patcher UI. The main window was meant for a higher purpose, but I had to rewire things at the last minute (to keep my 48 hour promise on the news page) and it kind of lost it's edge.
Beta 1.1 will do some things differently, and include a neat idea I just thought of to kind of supplement the lack of mod launching in the 1.0 release. You'll be able to add shortcuts for JK.exe to the tray menu of JK Patcher, so you can launch either patched exe with a -path statement. An Easy JK Shortcut Manager if you will.