Round 1:Flying Muto Vs.Gigan 2004

2004 Gigan.

Gigan, he posed a good threat to the strongest Godzilla incarnation, while this MUTO didn't do any real damage until the female showed up

really i have to say MUTO

Assuming the EMP doesn't effect Gigan Gigan would win. Honestly I think Gigan is severly overrated by most people in terms of strength, but this basically comes down to the MUTO having nothing that could actually kill Gigan, while Gigan has so many way to kill the MUTO