Smashwords used to allow less keywords than Pubit, which meant a Pubit book had a better chance of finding readers via keyword searches. I think Pubit allowed longer descriptions, too. I know these were issues Smashwords was working on, but not sure where it's at right now.
Two edges for using Smashwords over Pubit: higher royalty on books outside the $2.99-9.99 range (so for instance, if you're writing 99 cent short stories, use Smashwords - income is 60% instead of 40%). Also, all Pubit books have the "Pubit" logo and a button users can click if they find the content offensive or problematic. If the Pubit logo ends up associated with bad quality books, not having that logo might be valuable, and Smashwords books have neither - there is no visible difference between a Smashwords ebook on B&N and an ebook from any other publisher.