I'm going to re-suggest an idea that I've brought up many times - the idea of protocol sections.

It's a way to break up a big protocol into pieces. The sections could be displayed/hidden with a click; likewise they could be turned on/bypassed with a click. I use filters and globals to accomplish the latter, but this would be slicker and faster. The former can only be done with subprotocols, but then you have to double-click them and then move between windows, which is clumsy.