The current way that permissions are handled on prims is very cumbersome. ESPECIALLY WHEN BUILDING AS A TEAM. I would like to propose the following:
On bulk upload (textures for example) allow the permissions to be set before the upload begins so that it is not necessary to go back to every item in the back and click all the buttons to set permissions to all.
Give us a preference for the DEFAULT PERMISSIONS of all of our newly created items. I am mostly working with a partner these days, it would be helpful to me to be able to say in my preferences - "Ok, everything I make right now has full perms until I change this setting again". In large builds it is SO difficult to catch every little prim and set it. I want to just be able to create and not worry about this crap until the end when I am done.
Add some sort of "cascadability" to permission setting to allow multiple items to change permissions at once. I realize you can select multiples and sometimes you can reset them all at once, but the process doesn't seem to work consistently for me. For example, the ability to change all the permissions on all the children prims in a linked object, so that if unlinked all of the prims keep the permissions of the top linked item. I want the ability to apply permissions from the top down - "apply perms to this object and all its children".
I find the way the permissions work on scripts inside my prims when working at a team to be completely counter-intuitive. My partner and I have been having serious issues when he adds a script to one of my items and then they wont be editable to me or cause other problems with the prim. The only thing that seems to work is to have every box checked in the perms, but this leaves us with the question of what happens for the next owner of our objects. The problem seems to stem from where I am the prim creator and he is the script creator.
I almost wish there was another level of trust for "mod my objects".... It would be scary but... it would be helpful to be able to give a partner builder full "treat him like he's me" rights to the things I am building. Just the objects i am the creator for (not things i own necessarily) - so that if my building partner wants to copy a window i made and use it elsewhere in our build he doesn't have to worry about if i have set the rights or not. But this last thing may open other cans of worms. I think that if i had a way to set the preference for the perms on my prims overall as i am making them that this last thing would not be necessary.
As to your problem with scripts: when your partner drops a script into an object you own, an ownership transfer is processed, and the script's next-owner permissions are applied. This means that the script will lose permissions if you're not careful. Also, if your partner didn't click "Share with group" in the SCRIPT'S permissions before dropping it into your object, he won't be able to edit the script once it's in your object. It all makes sense, but it definitely is cumbersome.