I can not help tendering to you one thing that would make Merger Science more dynamic and would perhaps not swallow up too much programmer time.
Yes, I totally agree, colors can help make the simulations much more interesting.
To add colors to the simulations to represent the observed colors would require much more involved calculations including gas and stellar evolution. However, there are several other ways to incorporate colors. One is to assign an arbitrary color to the particles belonging to each galaxy. That allows you to observe interesting effects, such as mass from one galaxy being captured by another. This can sometimes be confusing for people observing the simulation.
There are two ways that we do use color in the current merger applet. Both are accessible from the enhance tab. To activate them, right-click (or shift-click) on the big simulation panel. You will have options to blur the image, color by z-velocity, and one other. The color by z-velocity option will show the particles moving towards you as blue, the ones away as red, and the ones in the middle as purple. There is another color option, but you need a certain type of eye wear to take advantage of it.