Hello Jason, I particularly prefer that the hydrogens are all explicit with the option to make them implicit at any time. I had some minor problems using MoleculePlot, because I prefer that hydrogens automatically appear in all molecules of a series of symmetrical molecules that I created, I programmed the hydrogens to have a different color, but they appeared (visually) only in methane and I wished they appeared in (e.g.) many halomethanes, etc. in the 2D view and wasn't sure how to do it. At least that's what I felt. But I found that both MoleculePlot and MoleculePlot3D are really amazing functions!

Another difficulty I had using MoleculePlot and MoleculePlot3D is that I could not differentiate the clockwise and anti-clockwise spatial isomers of for example {C, H, F, Cl, Br} in visual representation. I just couldn't do it just by changing the order (the way I imagined), they looked exactly the same. I wish it were easier to do this, such as changing the order in the list. I may be wrong and this is easier than I think, but I couldn't do it.