Symptoms: Papers2 uses high amounts of CPU usage and memory while it is apparently doing nothing.
Reason: after you have imported a large batch of new entries into Papers it will start processing these in the background so you can continue to work. Depending on the type of entries there's little or much work to do. For example, if the PDF you import doesn't contain any text it will try to perform Optical Character Recognition, a very CPU intensive process. Papers will also Spotlight index the PDFs and render a thumbnail.
Solution: simply to wait till Papers is done. Eventually all processing will finish and will stop consuming memory and CPU load. Especially after just upgrading from Papers1 or after importing a large batch of new documents this process can take up to a few hours.