I think that someone already suggest it before, but anyways: How about a toolbar for "drawing" of the particles (as in Paint): free brush, line, filling tool, empty / filled rectangle, empty / filled circle and may be something else? I think it will be much more convenient to create simulations.
I asked somewhere before without real answer. Actually it is a request made for the original TPT by someone else:
The brush circles always have one pixel on each side that stands out. Would it be possible to make the circles better circles, thus, removing that one pixel? Edit: And allow a LARGE radius, which would eliminate the need for the circle tool
(And while we are at it: Make the box tool create real boxes, which are not one pixel larger than what is actually drawn, and no soft corners )