Yes the slow attacking is to do with moving targets, unfortunately the client has trouble attacking moving targets, im not the only Dev who has raised this issue. I have tried a few things to combat this issue but any that have worked have caused other issues, it is on my TODO list to come up with a proper solution to this, this issue is worse the faster a target moves.
As far as the burying bones, the speed at which it buries is as fast as Runescape will allow, If i make it quicker it will then click before it has finished burying the last bone and then have to reclick. I can add an option to bury during combat, this will help with your prayer in the catacombs.
Its actually not that weird, the majority of people will sort their inventory rather than just having a big mess. I can add an option to disable this for those who do not want this feature.
I will have to look into the pet hovering, im not to sure why it would do this. Can I ask which pet it is?
Unfortunately there is no way to tell what loot belongs to you or others, I already explored this option along with some other devs, and the only way that has been developed was extremely process heavy and would cause massive issues. To combat this issue I have created a method that will only try to loot an item once and if it does not belong to you will not try again. I have also added an option to set a loot radius around the target, This means it will only loot drops that are in the immediate area of the last target.