I bought a Prime a few weeks ago with the hopes of replacing my iPad with it. Superior specs at the same price plus one less Apple device. However the stylus performance was the killer feature (in this case the feature that killed the Prime for me). I have four different stylus's including Boxwave, Targus and a couple others. None of them performed worth a darn on the Transformer. This feature alone is something I use the iPad for all the time - taking notes with a stylus.
I was willing to forgive the lack of decent stylus apps since these can be developed over time. However, with the hardware just not detecting the stylus that's not something that can be fixed in an app. Played with the Prime for a day but ended up taking it back to Staples and getting a refund.
I'm not done trying out Android tablets, hopefully this is just something with the Transformer's touch screen design. I would love to see an Android tablet with digital stylus support some day.