Depends really on how your going to be using each squad, because if its an anti-tank squad you may want to keep a flamer in there to ensure that any enemy infantry approaching can be driven off. Vice versa with the meltagun and anti-infantry heavy weapons. In general though you're wasting the potential of at least one of the weapons by mixing.
Now 2 assault weapons is just double the fun, I was walking home from my mate's last night and an idea came screaming into my skull: Plasma Gun & Flamer.
I know the Plasma isn't an Assault weapon but hear me out- its the perfect combination to kill MEQs in cover because of that most blessed of things, armour saves.
There are 3 different saves you can get, Normal armour, invulnerable saves, and cover saves. But you can only pick to use one for a squad. The joy with Plasma/Flamer squads is that if the Marines (for example) choose to use their armour saves then the plasma can cut straight through their armour. If, in fear of this, the marines use the cover save (unless they're in a bunker this will be 5-4+) the flamer slices through that as well. Pretty much a win-win situation for you
Just a thought