@Kevin: I think a lot of that comes back to process and client education. Mock ups aren’t the only tool in our toolbox, and they shouldn’t be doing the work on their own. At Happy Cog (and personally), we do all of our wireframing in HTML, and that’s where we work out things like layout, responsive states, and interactions. Those prototypes are the things that get our native web thinking communicated.
Our mock ups are where we establish the graphical side of things. We don’t make mock ups for every page or state—just enough to communicate the graphic style of what we’re building. So as our process has changed, we started using different tools to communicate different things. We do a lot to educate our clients on what purpose each deliverable serves, and that’s one of the most important things to establish with your clients early on.