I think a few of these are being looked into by the devs. I can not find the link, but they did address the issue of linkshell management here:

http://forum.square-enix.com/ffxiv/t...727#post210727
and here:
http://forum.square-enix.com/ffxiv/t...ll=1#post84754

I think they are trying to take care of these issues as they go along. They didn't specifically address a few of your points, but I am sure they know about them. They have been mentioned before.