Yup, all copy or dublication processes generate new objects that you’d have to delete, which is ultimatively just like an undo, but this compromise, even while it’s not a great one, keeps the general workflow faster at this point. However, we’ve been kicking this one around for some time now, because ultimatively we could arrange for an undo that would save and recall entire scene informations and then none of that would be a problem anymore, but everything would be a little more at the speed of most other applications in that regard. I think I wouldn’t mind it all that much, because I actually don’t undo that much in messiah…only tweaks if any and there’s no problem at all. Strange, I know…hmmm…but, yes, don’t worry, this is something we have on our mind.
NOW for the good news:
Shadernode list acts beautifully and straight forward now. If you delete the last shadernode in a material it now stays fine within the material and doesn’t jump to the next one.
New particle emitter visualisation is accurately representing the particle emission area.
Lightcone angle is viewable and adjustable in object-view mode (looking through light in this case).
…and more things, I think…can’t think of it right now…lot’s of stuff.
I’m also adding a new particle force, which is quite fun! 
I’m grabbing the new stuff you’ve listed now and see that we go through it, too! :wip: