I am really happy with the addition of iTunes/iPhone support. I've been using it to put my shows on my iPhone and it works great. My only issue is that it places the low rez h.264 files in the same directory as my main recordings and then they show up in BeyondTV's front end when I'm browsing all my shows.
I would like to be able to tell BeyondTV to put my iTunes shows in a different folder. I would also like to be able to make the folder "hidden" from the beyondtv front end in the folder settings. This way I don't end up with every episode listed multiple times. The ability to "hide" a folder could be useful for anyone who has showsqueeze settings for mobile versions of their shows that they have no desire to view on their tv, not just the new iTunes integration.
Another thing that would be helpful would be to make the iTunes format dropdown a series of checkboxes instead so that BeyondTV would make 2 seperate versions each with their own RSS podcast. Heck some people have an iPod, iPhone and AppleTV... freaks that they may be