Based on my own experience of using both I can make an honest comparision of the 2 save actions.
For all the rest: navigation, opening, and so forth I only use P3DO, except to replace Figures which you can't do with P3DO.

pros

• saving poses with no morph is easier
  
• faster on saving - don't have to click on several dialogs to save your asset
  
• refreshes faster (have to hit F5)
  
• faster to navigate and save in various libraries
  
• alternatively you may save anywhere
  
  cons
  
• less options than saving with Poser
  
• no partial poses
  
• can't select list of materials
  
• figures are saved with parented figures
  
• can't save more than one prop
  
• you have to hit F5 to refresh
  
• it is a bit difficult to figure out how to save in Poser from an external software. Something you have to do a number of times to get accustomed with
  
  I am still using both, but I am using P3DO save more and more and Poser only when I need a missing options.
  I plan to add those missing options in the future. The reason they are not there is because the Python API is not providing them. Up to now there was no real need since the Poser Library Palette was there to assist :)
  

Yarp - author of P3DO Organizer for Poser