" @DEGRAAF:   Captain Atom's power source is the Quantum Field, a limitless void composed of all matter and energy.  Firestorm's power source is the Firestorm Matrix.  Both have the ability to manipulate matter and shoot energy blasts. However, Captain Atom is more accustomed to energy blasts, while Firestorm is more accustomed to atomic transmution (although both of them can do both things). Firestorm can become intangible. Captain Atom cannot. Captain Atom's ability to use the Quantum Field is mainly based on his will, and I don't think the same is said for Firestorm using the Firestorm Matrix. Captain Atom possess superhuman physical attributes on a much greater level than Firestorm (Class 100+ strength, near-indestructible durability, light speed flight in space, etc). Captain Atom is generally more powerful than Firestorm, having defeated Firestorm (Ronnie, while merged with Stein) in battle on two occasions. Against Jason, I don't think the outcome would be much different.  However, since both Ronnie and Jason are now one as Firestorm, it could be argued that they are more powerful than Captain Atom now, since they are powerful enough to trigger than Big Bang... "

I think this is the main difference. Both have energy and matter-related powers, but Firestorm is required to know the chemical composition of whatever he transmutes. That I know, this has never been established for Atom (has it?). But the source of their power makes all the difference, since the Firestorm Matrix has recently been stated as having ties to the Big Bang.  "

@Silver2467: In referrence to Captain Atom's ability to manipulate matter, Captain Atom, even though he's shown to be capable of using this ability, claimed that he wasn't very good at it. To be generous, I'd say that his ability to manipulate matter (transmutation and the like) is mid-tier, at best. In comparison to Firestorm, limitations aside (and not counting the Brightest Day version, whose transmutation abilities happens to be limited by Ronnie's lack of intelligence), I'd say Firestorm fares better than Captain Atom as far as matter manipulation goes. 
 
@entropy_aegis: The Blackest Night version of Firestorm? Absolutely. He's not that much different from Jason Rusch Firestorm. Hell, Captain Atom defeated a magical evil version of the Elemental Firestorm during the War of the Gods event (Shadowstorm). Elemental Firestorm was already more powerful than the original Firestorm also...

@DEGRAAF: Captain Atom is referring to himself in the 3rd person. The part about him mentioning that Captain Atom beat Firestorm before was the previous fight they had in Captain Atom #5 (which is the first fight posted before the second on in question).