Same old, same old: You are using temporal effects and rendering to a clip format - all of which require strictly linear processing. Looking for the magic button? It doesn't exist. Everything perfectly normal and I've had worse than 3 minute projects rendering for 3 hours. Check the forum, plenty of threads on teh subject and also read this:
You should not be rendering h.264 movies from AE's render Cue. Use the Adobe Media Encoder for rendering to delivery formats. Everything Mylenium said about compressed formats taking a long time to render is true. The only way to speed up MPEG encoding is to buy a hardware compression solution. Those don't fit into production pipelines very well.
See this page for resources about making After Effects work faster: http://adobe.ly/eV2zE7
If rendering stops using multiple cores at some point in the composition, it is likely because that is when an effect, expression, or other item that is incompatible with Render Multiple Frames Simultaneously multiprocessing begins. The link that Mylenium gave points to a page that lists some such effects.
A few hours is not a long render time for a movie that includes a denoising effect and color correction effects.
Regarding encoding from After Effects: The best way to work is to export a losslessly encodeded master from After Effects and then use Adobe Media Encoder to transcode that. The watch folder feature of Adobe Media Encoder makes that last step automatic once you've set it up.