i had this exact dilemma and i decided to go with the sony t1 because it had an audio jack (you can listen to audiobooks, pandora, etc) and hardware home + back button (from pics i saw it didn't look like the nook had a one or the other). what attracted me the most, however, was the sony's stock internet browser which works amazing on it's eink screen compared to opera on the nook.
the biggest con is that the sony reader fully refreshes the screen (blinks black) when scrolling unless you install a app on the sony board that allows you to toggle it to partial refresh (like what the nook has). i find myself having to toggle it very often which gets annoying but i try to adapt. just scrolling through menus would be hell without the partial refresh.
basically if the android apps you are looking to get the most miles out of requires lot's of scrolling and zooming, the sony might not be the better choice. for instance, difficult to use apps like cool reader, officesuite (to view word docs), which the nook does a better job at rendering. the sony stock apps are amazing enough though, at least for me, to outweigh it's limitations as a rooted android device.
check this video out
http://www.youtube.com/watch?v=rYC2GBhWJAs