Depends on what you want to do.
If you want to synch your email across devices, go with IMAP. That way, you can delete an email only once and it will be deleted across all your devices, for instance. If you use POP, you'll have to delete the same email on each device.
I prefer POP, because I don't want my email synched. I prefer to file and otherwise use my email more broadly and longer term on laptop, and on my mobile devices, I use emails only short term. I have thousands of emails stored on laptop. I have about two or three dozen on iPad at any given time, for example.
The best choice is whatever meets your needs.