Based on the current reports, looks like paper applications are faster. But IRCC would have spent a portion of its budget to create the online application system and will likely extend the online system to all applicants.
While it may slow at this time, I believe that IRCC will pour in resources and make the online system the only way to submit citizenship applications in the not so distant future. Online applicants might see a good improvement in processing times eventually (again, not very long from now).
Its really up to you but if I were to choose between the two, I'd take the online route.