First off, I am absolutely loving the new Web Editor; I am currently in a business start-up that uses Arduino boards and the Arduino IDE and it has been extremely helpful. One thing that I would love to see is some kind of Team or Business collaboration feature. Right now I just have multiple people signing into my account to edit the code.
Second, I find it frustrating having to import all of my custom libraries previously on my desktop IDE into the Web Editor one by one. Adding an Import all feature would be fantastic.
Lastly, I just switched to the web editor and I'm already missing the library manager feature in the desktop version that allowed you to simply search and download new libraries.