Is it possible to skip or exclude a PortableApp from being updated?

You should absolutely not stay with Firefox 28 as Firefox 29 includes multiple *critical* security fixes. If you continue using Firefox 28 after today, you're taking an huge risk with your entire PC.

If you don't like the Australis layout, you can customize it using an extension like Classic Theme Restorer and other extensions. If you have an incompatible extension, just disable it until the publisher gets around to updating it.

As for preventing the updater from updating an app, just uncheck it. In a later release, unchecking it and clicking Next will cause it to remain unchecked by default and prevent it from triggering an automatic update notification. But we will not be implementing a way to entirely hide an app from the update other than renaming due to the security issues around not updating.