First of all I have to say that roll20 is bar far the easiest to use and most powerful virtual tabletop I've ever used.
I would like to see a few improvements to make it easier for some of the FATE based systems as well as a wider use of the Characters panel. I would love to see some synergy with Tokens and the Character panel. I understand that there is some hesitation of putting stats in that area, but I'd love to see the ability to assign a specific token to a character sheet so that Players may drag and drop themselves onto the table easily. It would also allows GMs to plan ahead and have their tokens linked to the NPCs they created, just in case.
On the FATE front, I absolutely love that you guys built in the dice to the system. It really simplifies things for some of my players. I would like to see some stress tracking built into the game if possible. Stress in Dresden Files and other FATE games is a building system of boxes that once you take that specific damage, you can't take it again and the damage increases.
What I would LOVE to see for FATE or other systems that rely less on the tabletop is something akin to a Stat bar. Something out of modern MMOs where you would have your Character Portrait to the left and the Stress Track moving out from the right. I could even see this being able to be used easily with the Token System. Just add some new code to use and track stress and let the player use a portrait instead of a token.
A numerical value could be placed on each stress track to see how high it goes. This will create the boxes on the Token. Then it's a simple click on the stress box to fill it.
Thanks for your time, I can't wait to see where the system goes next!