Hi Axmann,
Welcome to Vista Forums!
First, Vista is quite different from XP. You can't really give the Administrator Account access to EVERYTHING on the PC any more. Removing Extender won't help because the removal/uninstall process does not know how to restore the original permissions (as that information was not saved and thus the changes cannot be undone). System Restore doesn't work because it does not affect data files (intentionally). There's no way to return to the way things were at this point without doing so manually - and if you intend to use Media Center and the Extender properly, you probably do not want to make changes to those files (getting permission is one thing - actually using it to alter things is quite another).
Some folders are actually not real folders but junction points
Svrops.com - Windows Vista Junction Points and shouldn't be touched by anyone but a true professional who knows exactly what he/she is doing - and over 99% of people don't fit that description (not even me). Some folders contain system files which even Administrators shouldn't touch without risking damage to the system (again, without the proper knowledge). This was done intentionally and the safeguards are pretty strong so only someone VERY familiar with permissions and ownership can override the restrictions (and sometimes only by making somewhat drastic and unsafe global changes).
In this case, the changes were made because controls for access to these files (and their location and file properties and such) were re-located with the installation of Windows Media Center Extender so it amended the permissions at the same time so the user wouldn't accidentally mess up the ability to use Media Center properly for searching and sorting and so forth.
If you want, we can change things so you can get to all the files in your Documents, Pictures, Videos, Audios, Downloads and any other folder IN YOUR USER PROFILE DATA STORAGE FOLDERS as either an Administrator or using the standard user account
for that profile.
Login as an Administrator and go to the folder you want to change (say "Documents"). Right click on the folder and click on properties and then click on Security. In the Upper section where it lists people with access rights, simply add your Administrator account (and if in a standard user account profile, add that user's account as well) with full rights. Click Edit and then Add and then add the accounts. Next, click on Advanced and go to the Special Permissions section and essentially do the same thing (but here, be sure to check the box to apply the changes to all sub-directories and files). Save the changes and that should take care of the problem for that folder. Then you need to do essentially the same thing for any other folders you want to change in every user account where you want to make the changes. Then you'll have access again; however, you also risk messing up Media Center if you make changes to these files directly in Windows Explorer - but that's your decision and your risk to take.
In case you run into difficulties, here's some additional information on permissions and ownership which may prove useful:
To see your permissions, right click the folder/file, click on properties, and check out the security tab. Check to see what permissions you have by clicking on your username (or user group). Here are the types of permissions you can have: http://windows.microsoft.com/en-US/windows-vista/What-are-permissions. You need to be an administrator or the owner to change permissions (and sometimes being an administrator or even an owner isn't enough - there are ways to block even them from access (though a smart administrator knows these ways and can get around them - but usually shouldn't because they were denied access usually for a very good reason). Here's how to change folder permissions in Vista: http://www.online-tech-tips.com/windows-vista/set-file-folder-permissions-vista/. To add take and grant full right permissions and ownership to the right click menu (which will make it faster to get in once it is set up), check out the following article: http://www.mydigitallife.info/2009/05/21/take-and-grant-full-control-permissions-and-ownership-in-windows-7-or-vista-right-click-menu/.
To fix this problem with the folders, take ownership of the folders or the drive (as an administrator) and give yourself full rights. Right click the folder/drive, click on properties, go to the security tab and click on Advanced and then click on the Owner tab. Click edit and then click the name of the person you want to give ownership to (you may need to add it if it isn't there - or it may be yourself). If you want it to apply to sub-folders and files within that folder/drive, then check the box for replace owner on sub-containers and objects and click OK. Back out and now there's a new owner for the folders/drive and files who can change permissions as needed. Here's more information on taking ownership of a file or folder: http://www.vistax64.com/tutorials/67717-take-ownership-file.html. To add take ownership to the right click menu (which will make it faster to get in once it is set up), check out the following article: Context Menu - Take Ownership.
Good luck and I hope this helps!
P.S. I would recommend you spend some time reading up about how to use Media Center and Media Center Extender so you'll understand why these changes were made in the first place and the risks you are taking by making changes to those files using Windows Explorer.