It has been a long time since I used Roll20 (I am still waiting them to accept Paypal for payment instead of having to send my credit card info to an unknown company).
So, I was quite sure that isometric gaming was not possible with it. But...
Since my last visit they have added a feature called Rollable Table Token and that's just what is needed to play with isometric figures.
Here is the result:
It works quite easily. All the stuff made for Maptool would work with it (I think, I am not a specialist).