Whether you should use Omega 4.x or Omega 3.x really depends on how much you want to rely on the user interface for building layouts as this is no longer included in the 4.x branch. If you are okay with a possible lack of documentation and the fact that Omega 4.x does not come with a layout builder as 3.x did then you should definitely prefer the 4.x branch.

Differences between Omega 3.x and 4.x

The Omega Drupal 7 Base Theme is a highly configurable HTML5/960 grid base theme that is 100% configurable. Each zone (group of regions) can be configured for content first layouts (push/pull classes), hidden at any time and each region can be disabled, resized, and placed easily any way you see fit.