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yeah, depends what level of interaction you're looking at and what you're using the prototype for really. I use Invision for user testing, as you can create sticky headers, links, transitions and the like - but you can't really create loading animations or micro-interactions.

If you're just trying to show how transitions and interactions work, you're probably better off using After Effects. If you're trying to create an interactive high-fidelity prototype, there's a bunch of tools that work ok but you've either got to double-handle assets (design in photoshop, rebuild in Axure / Justinmind) or wire it up with code (Javascript, various Node.js kits) or something in the middle (Edge Reflow).

Depending on how much code you're comfortable with, there's a bunch of Quartz Composer-esque tools that will allow you to prototype more complex interactions like VVVV, Max/MSP or TouchDesigner - but at that point, you might as well be prototyping in code directly.