What is the difference between Unity-2D and Unity-3D?

Technical differences.

Unity

• Written in C++ as a compiz plugin and uses nux for OpenGL support.
• Requires hardware acceleration (Compositing). (Hardware requirements)
• Is shipped as the default environment in 11.04
• Also does window management via compiz itself.

Unity 2D

• Written in C++ with Qt
• Works on systems without hardware acceleration, like ARM-based platforms, as a result it is incapable of advanced 3D effects.
• Shipped as the fallback method in 11.10. Is not shipped by default in 11.04, available as a separate package that the user has to install.
• Needs a seperate window manager (like metacity) to do window management.

Unity-2D is for use with computers that do not support 3D-accelerated graphics, such as some low-end netbooks. Unity-2D looks almost exactly the same as its 3D counterpart, albeit without a bit of the eye-candy.

As for updates, both should be updated around the same time - although I'll expect Unity-3D will have a bit more effort put into it just due to the fact it is the "mainstream" version of Unity.