Why show articles in a grid instead of a list? A list makes the hierarchy clear, and is easy to parse.
Why have articles text on multiple columns instead of one? Multiple columns are a left-over from print newspaper who had to use them for practical reasons. I personally find them less readable than a single column (except maybe for very short articles).
Why prevent me from zooming in or out to adjust the font size? This is actually one of the coolest thing about browsing the web on the iPad, and you break it.
I think it's a shame, because I really like some of the other features, like the preloading of the content, and stripping away the ads and distractions.