Red Alert 3 is the first game in the series to use a 3D engine, resulting in graphical improvements. As a result, Command & Conquer: Red Alert 3 is a direct sequel to Red Alert 2, and can be considered entirely distinct from 2007's Command & Conquer 3: Tiberium Wars.
The Command & Conquer: Red Alert series takes place on an alternate time-line to the main Command & Conquer series, forming a separate continuity. The Red Alert series gets an upgrade in this 2008 sequel.