First, I applaud anyone showing an interest in focusing on the interaction side of design. In corporate UX groups, I find that the one thing that often does fall through the cracks is the interaction design (often due to waterfall development processes). The UI may look stunning, the back end, tight and responsive, but then you put them together and things still feel clunky because no thought was put into the transitions, or hovers, or animated reveals, etc.
So, any UX team that would have you, would be an excellent UX team to be a part of as there is clearly consideration for this.
As for what tool to use, that's where I get a little more skeptical of anything but the actual medium one is working in. I'm a strong advocate that if you're working on prototyping motion for a web app, use the medium of HTML, CSS, and JS to do it. If it's a native iOS app, grab Quartz Composer and use native animations.
That's not to say After Effects isn't a great tool, though. Ultimately, it's the person behind the tool that's key. That said, when only the tool is used, teams can get overly reliant on the interactions that exist only within that tool. For example, a team that only uses Axure may end up unknowingly creating web sites that simply feel like default Axure interactions.
SharePoint is another good example...it takes a herculean effort to build a SharePoint site that doesn't 'feel' like SharePoint because you're stuck within the medium of SharePoint.
do you see a use for someone to come in, like myself, on a freelance basis to prototype motion in AE?
Do I? Absolutely! And hopefully other UX teams do as well.
What other tools do you find beneficial for this?
I'd start playing with jQuery. Get your hands dirty with some JS and CSS3. Even if you don't ultimately work in that, it will give a lot of great context to take back to better create your After Effects work.
Other popular tools that include different forms of interaction prototyping that UX teams use:
- and (again) HTML, CSS and JS.