Why Ubuntu wiki runs on different software to other help sites?

The Ubuntu wiki has recently been changed to use a new theme that fits far better with Ubuntu's new visual identity - new logo, colours, fonts, etc - the same things you'll see on this very site infact. For more details take a look this blog post from Mark Shuttleworth that introuduces the new visual feel.

Having said this, the new theme is probably not perfect yet - I would say it lacks the polish the old theme had.

The official web documentation has not yet been changed to use the updated visual identity, but I assume it eventually will.

If you wish then in your Ubuntu Wiki User Preferences then you can change your theme ("ubuntu" is the old one, and "light" is the new one).