Angie Taylor explores the question using Premiere Pro as a real-time engine for After Effects. Her exploration echoes an earlier observation by Jarle Leirpoll, noted in Premiere with CUDA for compositing...
... a lot of the basic compositing you do in AE can now be done in real time in Premiere Pro. ...With all the basic stuff in there, like Transforms, Blending modes, CC, Track Mattes, Green Screen (Ultra keyer is amazing) and the most used effects, Premiere Pro is quite capable of doing at least 75 % of the effects stuff I need. In real time. On several HD layers. And as an added bonus, export to web formats, DVD, Blu-ray etc. will be lightning fast compared to AE.
One might also add that there are also quality gains by using a CUDA card. At least one person noted though that rendering hefty AE project sections through Premiere then onto AME takes longer than exporting from AE.
It's a rarely mentioned topic, so hopefully Angie can continue to clarify the boundaries of what works best for what tasks.
By the way, The Genesis Project has 2 good tips for Premiere Pro CS5 maintenance, and one of them may help with the naughty bits of conformed files. For more info see Dynamic Link for the AE Workflow (an overview by Andrew Devis), optimizing for performance: Adobe Premiere Pro and After Effects by Todd Kopriva, and Working with Adobe Premiere Pro and After Effects in AE Help.