I have owned a Nexus 7 for about a month and use Aldiko. I love it! I have been using Dropbox to transfer books from my desktop, which has worked out very well. I prefer to only keep 20 or so books on my readers and store my entire library on my main computer.
I will never give up my Kobo because it is the perfect companion on my camping trips - long lasting battery life, fits in a zip lock for rainy days...you get the idea. The Nexus is fabulous to use on the safe environs of my couch, but I am reluctant to expose it to the elements.