I've tried Project Comet and I have to say, though it is not even close to shipping, it is awesome to have design and prototype features in one tool. What you haven't mentioned in using two different tools is that when you want to make changes to your design you'll have to export again, import into your prototyping tool and then add functionality again. I totally agree with you that just having basic "connect-one-screen-to-another"-features is pretty useless for presentations.

I love Layout! Great job guys.