Amjoie the plants - like the rugs are fine. Look at it this way - if you click on a object and the only reaction your sims get is veiw - then 99 percent of the time that object is okay to Moo - but in the scheme of things keep in mind the space the object will use if not mooed as sims will not see the space you have freed - they see things as if no moo was ever used - so just test it. But you are almost always fine mooing things that sims can only view or never inter act with.
Regarding ghosts -
Like I posted I am not sure if it will work with Sims ghosts not on your lot, but keep clicking on the ghost sims and see if they get the option to go to the Netherworld - if they do - say yes and they will take their tombstone and permanently vanish. (I have only sent ghosts to Netherworld on my home lot, and generally had befriended them and sometimes made them playable. But clicking on them eventually will give that option. Sometimes it takes a while though. It used to be easier.
Changing sims appearance and traits has not shown to ever be a problem. So change away. In fact EA made it easier to change appearance without getting problems when they created Salons and that career. It is made to do that just like plastic surgery is.
Deleting is easy - like I said because our sims we add to the game are not hardwired into that hood - just like we can add them - we can delete them - but you want to only try and do that with sims who have not formed any real relationships in the game. If EA made no way for us to delete our own sims - that would stink. I know I have made my share who looked perfect in CAS and in game went all freaky looking. Not so much now a days, but in the early days - oh my sweet Lord they were gory.
