I'm assuming the desktop version is optimized for desktops, that now commonly have at least a gig of memory, fastish processor and so on. While Safari on the iPad is decent, it still has far less resources compared to a desktop or even a net book. Out of curiosity, how well does google reader work in desktop mode in the Nexus One?
I haven't dug into the code much, but it feels like google reader is using javascript for scrolling instead of letting the browser handle it, hence the need for two fingers to scroll.
If you do go with an ipad or other tablet, look for a dedicated app. I see 9 ipad specific ones searching the app store for "google reader". I can't really comment on any of them though, since I still don't use reader or orhter RSS services.