Actually, there are 2 manga lines. One featured in weekly Shounen Jump which was Fummofu and the other one which was what the original TV series was based on.
I absolutely hated the 1st season undertaken by GONZO. GONZO being GONZO takes a relatively good storyline and background, adds in 3d effects and stuff and cheeses the whole story off and ends it all with more cheese. Crap bad ending for FMP.
FMP:F was out of GONZO's hands....and I absolutely loved it, despite no mecha and being silly.