Apart from the U-He health warning, the biggest practical issue that I have come across is that by default, preset formats are different between VST2 and VST3. So if you cut across to the VST3 version, because it's all shiny and new, you suddenly find that your extensive library of presets is junk. This seems to be the case with Voxengo, for instance. Where the vendor uses a proprietary format, they apparently can sidestep the problem: FabFilter for instance seems to use the same format of preset.
BTW, I was a little surprised to find that Rapture Pro has no VST2 and comes as VST3 only.