You can get the latest version of Skype setup in MSI format from the following URL:
http://www.skype.com/go/getskype-msi

 Steps to Repackage Skype :

Create a transforms file for the vendor MSI and do the following changes.

 1) Remove the desktop Shortcut.

2) To Suppress the automatic updates, follow the below steps

a) Remove the feature "Updates"
b) Remove the Component "Skype Updater"
c) Ensure that Skype Updater Service is removed from the Services table
d) Ensure that "Install Update Enabled" and "Install Upgrade code" properties are removed.
e) Remove the following custom action:
   i) Skype Upgrade
   ii) Skype install updates.
f) Add a new component named as "AutoupdateSuppress" and then import the below registry setting:
HKEY_LOCAL_MACHINE\Software\Policies\Skype\Phone\DisableVersionCheck REG_DWORD = 1.
HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Skype\Installer\"InstallUpdates"=dword:00000000

g) Inorder to prevent the application from automatically launching during the startup, remove the following registry,
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\Current Version\Run

4)Add a new component "Activesetup" inorder to replicate HKCU registry keys and user profile data.
  If it is not added, the user profile data's will not be populated for new user as there is no advertised shortcuts. Also Send - to shortcut will also not be populated if we don’t add 'active setup'.

5)Step to suppress the welcome tour prompt which occurs during the second launch of the shortcut.
 The setting will get stored in config.xml file in %appdata%\Skype\%SKYPE USER NAME%\config.xml"
%SKYPE USER NAME% - Skype user ID (Don't get confused)

<?xml version="1.0"?>
<config version="1.0" serial="14" timestamp="1415790440.8">
<UI>
<General>
<VersionRun700Time>41955</VersionRun700Time>
</General>
</UI>
</config>

VersionRun700Time tag will help to disable the welcome screen.

But this solution works only if we have defined Skype user names, profile.Since we don't know the exact skype user names we will not be able to suppress this.Even the audio and video settings will not be suppressed due to the same reason above.

6) In order to prevent  file transfer through skype, add the following registry

HKEY_LOCAL_MACHINE\SOFTWARE\Policies\Skype\Phone added a dword "DisableFileTransfer" with value 1

The above said steps can be used for all the versions of skype (v6.11, v6.18, v7.3)

For more details check my Blog - http://app2pack.blogspot.com/
Happy Repackaging !!