Poshm,
The biggest reason is buying books from Sony -- only their manager can buy and load them. Cost compared to other stores aside, I'd keep it for their free books. They're still DRM'ed and you do "purchase" them. Will the device-lock change when Sony finally goes straight with ePubs? I doubt it, but who knows? In many cases you can get these in other formats from non-device-locked stores, but I've never confirmed it in all cases nor in a preferred format for the Sonys.
I'm also not aware of Calibre being able to create collections. It's not a required feature of the reader, and I'm on the fence about it's usefulness.
On the whole, I think Sony has done us a favor by keeping the software infrastructure somewhat open, unlike other devices. They do publish a software tool, but we don't have to use it to get almost all of it's functionality.
Dan <><
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