Re your point 2 You are heading in the same direction my company has gone. We have the equivalent of your 'Central System' as a Username, and have created three folders on its Drive - WORK, REFERENCE, EXTERNAL USERS - and shared them with our Sysadmin. Sysadmin shared WORK with Users on an Edit basis and our users built a sub-folder structure for our company to hold all our working files. Sysadmin shared REFERENCE with most Users on Read basis but with some Users granted Edit rights so they could create and maintain the folder/file structure for policy documents, manuals etc.

WORK is shared Edit and REFERENCE is shared Read to new starters as part of the User setup process and new Users immediately acquire inherited rights to all the contents of these folders.

Leavers, we change the User password immediately, use administration advanced tools to transfer ownership to their manager/colleague for any files/folders they may have created and then unshare them from WORK and REFERENCE.

We have not made WORK or REFERENCE to be the Owner of the sub-folders and documents which they contain because it would require that only someone logged into Central System would be able to delete them. We simply use our own version of Central System to provide a unified data structure for our Users. The Users each retain the 5gb of non-Gdocs storage space which is shared with other Users through WORK and REFERENCE.

We collaborate with external organisations and use EXTERNAL USERS as a portal. For example, our Auditors want access to our some of the data on our system. We created a sub-folder AUDITACCESS in the EXTERNAL ACCESS folder and granted our auditors' gmail accounts Read access to AUDITACCESS. We then use the Organise function to give them a View towards the files and folders which they need to access (but remember to hold the CTRL key down when you use the Organise function). This allows us to un-Organise files and folders, if necessary, since they are all listed in the AUDITACCESS folder and to un-share AUDITACCESS with our auditors email accounts, if necessary.

Hope this will give you a few ideas for organising your own system.

I installed Vidar’s script and works very well for files, but wouldn't reset permissions on folders. So, I changed a little bit the code to make the folders also inherite the permissions from their upper folder.

Two important disclaimers:

1. I don't know if the original intention was to leave folders unchanged. Or even if it worked well for everybody but me, and this solutions was unnecesary. It worked for me.
2. This is the first script I do, so it is very likely that it is not very efficient and may content some errors. Please feel free to correct it and improve it.

I only changed the doResetPermissions function, but I paste all the code for simplicity reasons.

var selectedFolder;
var dialog;

function doGet() {
  var app = UiApp.createApplication();
  var heading = app.createHTML("<h1>Folders for</h1>");
  app.add(heading);
  var allFoldersIterator = DriveApp.getFolders();
  var text = app.createTextArea().setName("text").setId("output");
  app.add(text);
  var tree = app.createTree();
  var rootFolder = DriveApp.getRootFolder();
  var treeRoot = app.createTreeItem(rootFolder.getName()).setId(rootFolder.getId());
  var handler = app.createServerHandler("folderSelected");
  tree.addItem(treeRoot);
  tree.addSelectionHandler(handler);
  treeRoot.setState(true);
  createBranch(rootFolder, treeRoot, app);
  app.add(tree);
  var selectedFolderIdBox = app.createTextBox().setName("selectedFolderIdBox").setId("selectedFolderIdBox");
  app.add(selectedFolderIdBox);
  return app;
}

function createBranch(folder, branch, app) {
  var children = folder.getFolders();
  while (children.hasNext()) {
    child = children.next();
    Logger.log("Folder id: " + child.getId());
    var subBranch = app.createTreeItem(child.getName()).setId(child.getId());
    branch.addItem(subBranch);
    createBranch(child, subBranch, app);
  }
}

function folderSelected(eventInfo) {
  var app = UiApp.getActiveApplication();
  var parameter = eventInfo.parameter;
  Logger.log("Selected " + eventInfo.parameter.selected);
  selectedFolder = DriveApp.getFolderById(eventInfo.parameter.selected);
  var selectedFolderIdBox = app.getElementById("selectedFolderIdBox");
  selectedFolderIdBox.setValue(eventInfo.parameter.selected);
  var okHandler = app.createServerHandler("okResetPermissions");
  okHandler.addCallbackElement(selectedFolderIdBox);
  dialog = app.createDialogBox(true, true);
  var panel = app.createFlowPanel();
  dialog.add(panel);
  dialog.setId("confirmationDialog");
  dialog.setPopupPosition(100, 100).setSize(500, 500);
  panel.add(app.createLabel("Do you want to reset permissions for all files found in folder " + selectedFolder.getName() + " and its subfolders?\n (Click outside of the dialog box to cancel)"));
  panel.add(app.createButton("Do it!", okHandler));
  dialog.show();
  return app;
}

function okResetPermissions(eventInfo) {
  var selectedFolderId = eventInfo.parameter.selectedFolderIdBox;
  var selectedFolder = DriveApp.getFolderById(selectedFolderId);
  Logger.log("Resetting permissions on " + selectedFolder.getName());
  var app = UiApp.getActiveApplication();
  app.getElementById("confirmationDialog").hide();
  Logger.log("Confirmation dialog hidden");
  var progressIndicator = app.createDialogBox(false, true);
  progressIndicator.setId("progressIndicator");
  progressIndicator.setPopupPosition(100, 100).setSize(500, 500);
  var label = app.createLabel("Working ...");
  progressIndicator.add(label);
  progressIndicator.show();
  doResetPermissions(selectedFolder, function() {
    var app = UiApp.getActiveApplication();
    var progressIndicator = app.getElementById("progressIndicator");
    progressIndicator.hide();
    return app;
  });
  return app;
}

function doResetPermissions(selectedFolder, callback) {
  Logger.log("Resetting permissions on folder " + selectedFolder.getName());

  var sharingAccess = selectedFolder.getSharingAccess();
  var sharingPermission = selectedFolder.getSharingPermission();

  var viewersfolder = selectedFolder.getViewers();
  Logger.log("Number of Viewers in folder: " + selectedFolder.getName() + " = " + viewersfolder.length);
  for (var i = 0; i < viewersfolder.length; i++) {
    Logger.log("      Removing viewer " + viewersfolder[i].getEmail());
    selectedFolder.removeViewer(viewersfolder[i]);
  }

  var editorsfolder = selectedFolder.getEditors();

  Logger.log("Number of Editors in folder: " + selectedFolder.getName() + " = " + editorsfolder.length);

  for (var i = 0; i < editorsfolder.length; i++) {
    Logger.log("      Removing editor " + editorsfolder[i].getEmail());
    selectedFolder.removeEditor(editorsfolder[i]);
  }

  var files = selectedFolder.getFiles();
  while (files.hasNext()) {
    var file = files.next();
    Logger.log("   Resetting permissions on file " + file.getName());
    file.setSharing(sharingAccess, sharingPermission);

    var viewers = file.getViewers();
    Logger.log("Number of Viewers in file: " + file.getName() + " = " + viewers.length);
    for (var i = 0; i < viewers.length; i++) {
      Logger.log("      Removing viewer " + viewers[i].getEmail());
      file.removeViewer(viewers[i]);
    }

    var editors = file.getEditors();

    Logger.log("Number of editors in file: " + file.getName() + " = " + editors.length);

    for (var i = 0; i < editors.length; i++) {
      Logger.log("      Removing editor " + editors[i].getEmail());
      file.removeEditor(editors[i]);
    }
  }

  var children = selectedFolder.getFolders();
  while (children.hasNext()) {
    var child = children.next();
    doResetPermissions(child);
  }

  if (callback) {
    callback();
  }
}