Hi!
First, I wanna say that I love this idea, a web-based IDE is an amazing development and I really love the design, it is so clean, congrats!
However, I have a few things to say about it:
1. Language support (I know it's a beta version yet).
2. You probably know the 123d.circuit.io page and I know that it's a huge project, but It will be nice to see the posibility to simulate the code or something similar.
3. The posibility to move the "Serial Monitor" view. For example, in another window (there are many people with two or more monitors) or in the same place that the "Verbose output" (in two tabs).
4. A button to copy the output of "Serial Monitor".
5. The posibility to make our own layout and schematic image in the IDE (or maybe import from Fritzing)
6. The posibility to install the Arduino bootloader in another atmega328p or another chip
I'm done... for now

Hope you found this things really usable.
Bye!