@billionaireman: I may be totally wrong, but this is my understanding.
Matter manipulation grants command of what is there. You concentrate on a tree and can cut it, stretch it, bend it, break it, levitate it, condense it, expand it, build a wicker man, etc...but it doesn't cease to be the remnants of a tree. Similar to telekinesis, but more like extending your will into objects to animate them. Selene is a good example.
Molecular manipulation grants command of what something is. You concentrate on a tree and can alter the chemical composition, wood to metal, metal to liquid, liquid to gas, gas into the Staypuff Marshmallow Man. It's no longer a tree, it's whatever you want it to be.
Both are only as powerful as the users' imagination and easily float in the higher echelon of powersets, but of the two, molecular is more godlike. Franklin has indeed reached the heights of godhood in one future timeline where Galactus is HIS herald, so I don't think it's a stretch to say he could bestow cosmic power to another similarly to Norin Radd's transformation into the Silver Surfer or create the perfect conditions to bombard some sad soul with Gamma Rays for a knockoff Hulk.
What mucks up the distinction between matter and molecule is his reality manipulation. It's practically both powers combined. Also, I think recently it was revealed he's not a mutant, but a legit Celestial.
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