AP: Ender Dragon. By a sizable amount. 25 kilotons versus 11.10 kilotons is noticable.
Powers and Abilities: Ender Dragon. Ender Dragon has regen and healing, acid manip, she resists Smaug's fire, and has attack reflection and intangibility. Don't see how Smaug is gonna hit it. Smaug has telepathy, but that's it.
Speed: Ender Dragon. Massively Hypersonic versus Supersonic+ is not good for Smaug.
Lifting Strength: Smaug. Not really too useful though.
Striking Strength: Smaug. For some reason.
Durability: Equal.
Stamina: Smaug.
Range: Smaug. Ender Dragon has extended melee range+, while Smaug has kilometers.
Standard Equipment: Equal. They're both very useful, as the Ender Crystals constantly heal the Ender Dragon, while Smaug's armor protects his weak spot.
Intelligence: Smaug. The Ender Dragon has seemingly average intelligence, while Smaug is dangerously intelligent, managing to maniplate and outsmart Frodo several times.
Weaknesses: Smaug. The only weakness he has that might come into play would be his arrogance. The Ender Dragon has a noticable and large weakness that Smaug can exploit, which is the ender crystals. Knowing how intelligent Smaug is, he'd figure out that the crystals are healing the Ender Dragon, and quickly destroy them. Not only that, if Smaug destroys a crystal while it's healing the Ender Dragon, it will take significant damage.
Notable Attack/Techniques: Ender Dragon.
All in all, while Smaug does take the advantage in many categories, the Ender Dragon takes it in the categories that matter most. AP, speed, and hax. I'm voting Ender Dragon with mid/high-difficulty.