Is there a reason why there are only 4 channels? I mean my mega has 50+ pins. So 4 is a little little.
SimPlot was intended to be similar to Oscilloscope than a Logic Analyzer. The 50 pins on mega are all digital pins and plotting the state of those pins is functionality of Logic analyzer. SimPlot is intended to plot analog values like output of sensors sampled by ADC, or values of internal variables etc.
That being said, it looks like there is interest for more number of channels. I will put in my to do list and increase the number of channels to 8. If there is interest in Logic analyzer capability I will look into adding that as well. Not sure how much interest is there.