Those are pretty different tablets. I'm not really sure how to compare them. Do you want 10" or 7"? What are you going to be doing with it: media consumption, browsing, gaming, reading, prouctivity? The screen on the Nexus 7 is better (same number of pixels on a smaller screen results in a sharper display). A 7 inch is much more portable, but you might want the extra screen size of a 10". If you want to be able to hold it with 1 hand go with the 7". Is having a really good keyboard dock important to you? You could get a bluetooth keyboard for the Nexus 7, but it won't be a good as the Transformer's keyboard dock. Also how much do you want to spend? The Nexus 7 is a lot cheaper. And with Nexus, you'll be the first to get software updates.
They are both great tablets. It just depends on what you want.