I got the Superman/Brainiac/Martian Manhunter set in the mail this past weekend.
MM is an all-new paint scheme. The straps, belt and cape clasps are solid paint, and the clasps and buckle are green. MM himself is also more green in color.
Here's a comparison. The new one on top, and the early 2006 3-pack version on the bottom.
And for fun, the various MMs made by Mattel using the 5-POA mold.
L to R: 2005 JLU single and 3-pack version; 2005 JLU Planet Patrol version; 2006 DCSH JLU MM 3-pack version; 2008 JLU 3-pack version; 2007 JL Original Members Collection version
Another thing of interest is that Mattel redid the packaging. It now features the new DC logo, and a different font for the text.