I love the NYT, totally agree with you. I just couldn't deal with the $240/year price to read it on my iPad and Browser, so I subscribed to the WSJ instead @$100/year.
Also, and I don't know if they ever fixed it, the NYT wouldn't include their business graphics/charts on their iPad edition. Very Lame. WSJ is good about including all their content on their (in my opinion) much more elegant iPad App.
I have a digital subscription to WSJ as well. It's worth every penny. NYT and WSJ probably complement each other more than they compete. I don't have an iPad so I can't really comment on the differences there.
