As a person who just switched from Kobo Touch to Sony PRST1, I can tell you that for me, the Sony wins hands down. I am not a very 'technical' user. I use Calibre to handle my library and purchase my books on computer and transfer through that. The reason I started using Calibre was for library management, I just found the Kobo lacking. Out of the box at least the Sony has a 'collections' feature, which if you don't want to use a library management system like Calibre, would be your best bet.
For me, the Sony is faster, and I've never had any problems in updates, managing library, etc. With my Kobo, I had a ton of problems [which is what brought me here], and yes, I everntually got them all sorted out. But so far the Sony has been so much easier compared to my Kobo.
Good luck and I hope you enjoy e-reading!