Flamer kills more infantry, uses 1 crit, and has no ammo concern
MG uses up 2 crits (gun+ammo), can be very destructive if the ammo is hit, but doesn't have to worry about heat.
i'd say it is a situational thing (space available, whether you want the option of a 'less-than-lethal' options like rubber bullets ,etc) but for anti-infantry, the Flamer is generally the superior choice.