I am not real familiar with the Kobo, but I've used my neighbors ever so briefly. In that brief period, I can tell you I much prefer the interface of my prs-t1.
I think that since you are using calibre, it will be hard to beat the sony for collection management. the sony will automatically add any books you have marked as a series in calibre into its collections area - and will sort the books properly for the series. I believe there is also an option in cailbre to have sony collections created based on genre and other tags you apply to your books in calibre.