That happens in every mmo. Look at Wow. Paladins were the best for awhile, then they nerf them to death and then lets say Warlocks were the best. Then they nerf them too much and something else takes its place. Im sure if you keep playing at some point mercs/commandos will be the best.
To the new changes, I love them. I still think SWTOR has alot of upside and is still fun to play. I think if they can work out the rest of the kinks and add more end game content, alot of ppl will either come back or start playing.