Sims apearing inside of other Sims, walking through Sims and not around. Saved commercial lot games.

That's just how the game is made as far as all of the sims standing inside of eachother when you load up the game. They made it so that sims can walk through eachother so there isn't so much routing fail. I'm not quite sure about your playable sims disappearing when you load to a community lot, though, because I built a hotel for my legacy sim to stay at while she didn't have a bedroom and saved and loaded to it many times and she was always there.