You can add autosave with a script see here (search is your friend):
http://www.inivis.com/forum/showthread.php?t=5938
(it should still work on later AC3Ds)
Saving the visibilty of objects might cause problems e.g. if you send someone else an AC3D file and it contains all sorts of hidden stuff, which they then export to another application. The main stumbling block is that it would require a change to the AC3D format. It's open for discussion here though.
The next release of AC3D will include wildcards on select-by-name
