First of all let me tell you how surprised I was when first trying Roll20. Considering it's relatively new it's got a lot of useful features which Iwill most definitely use in my groups.
However, personally I'm still missing a few things. Coming from the by now slightly dated MapTool, I have grown accustomed to using variables in my makros. For example, for Shadowrun I would love the option of using something like "/roll 'Dicepool'd6>5" which would result in Roll20 asking me to enter a value for the variable 'Dicepool'. Currently I use loads of makros for dice pools ranging from 1 to 20, with the same amount for GM-only tests and exploding dice (again both public and GM-only), a total of 80 different makros...
Secondly, the use of token specific makros in MapTool makes it rather easy to have all of a character's stats linked to the token. Other than having general makros each token would have their specific attack, skill or attribute stats.
Thirdly, although going back through the log can be nice, I have the problem that all my trial-and-error messages are still in the log and can't be deleted. Therefore a delete log option would be nice.
Fourthly, since my group uses a semi-public TeamSpeak RPG server, we hardly make use of the in-built voice and video chat functions. It would be great if Roll20 would "remember" the settings, i.e. don't use voice and video chat and only show player's name for the next time we open the campaign.
Finally, I seem to have some problems issuing a thumbnail for my campaign. It seems that the forward and backward buttons used to select it don't go through all of my image library. A manual upload function would be helpful with this admittedly cosmetic problem.
Truly finally, since we share the gm duties in one of my group it would be great if I could share the campaign file with the other gms, preferably without having to join Google+...
Reading through this posting it may come across that I don't like Roll20, which is far from true. However, these are points which would make it just much better.
