Two blog posts have been published on the Star Wars: The Old Republic site laying out big advanced class changes for both the Trooper-Mercenary and the Bounty Hunter-Commando. These two begin a series of articles designed to introduce players to the new 'Discipline' system and detail the specific changes players can expect when utilizing and playing in their chosen advanced class.
The Game Update 3.0 class changes for the Trooper and Bounty Hunter set of classes are, overall, the most drastic changes received by any class set in the 3.0 update. The term “class set” refers to the base class (in this example, the Trooper) along with its advanced classes (Commando and Vanguard, continuing with this example). The purpose of this blog is to inform Troopers of the major changes that are coming in the 3.0 update, but this blog is not a comprehensive list of every single Trooper change. Also, please note that the content described in this blog is still under development, so anything mentioned throughout this blog is still subject to change (especially any exact numbers or percentages that may be mentioned).
Read more about the Commando and Mercenary on the Star Wars: The Old Republic site.