You can't use AE animations directly except in the traditional "animated GIF button" sense. You can really only use it to demonstrate the desired outcome. The rest should not be your concern. Worrying about limitations would be detrimental to exploring new ways of doing things just like from a technical point of view it would be irrelevant - nobody would use your gigazillion keyframes, anyway, since programmatic relations rely on API functions and they surely will tell you what can and cannot be done once they come to that point...
After Effects and Premiere Pro do video. Video is NOT interactive. You should be looking at Muse and CC Animate (New and improved version of Flash) and other web prototyping tools. Video is absolutely the wrong tool to design and prototype UI for the web and mobile devices. The learning curve + the inability to actually preview interactivity exclude it from any reasonable toolset.
I use a ton of apps for that including a great little iOS app called POP (prototyping on paper) that lets you build ui and site navigation and designs from images or sketches in just minutes. I sketch things out for all kinds of projects with Mischief from Autodesk. There are a lot better tools for UI design.