Bagon line is going to give better results for most of the game purely based on the higher attack. Dratini runs 64 base attack into 84 base attack for Dragonair. Bagon starts with 75 into 95 at Shellgon. Shellgon is also going to give you a higher base defense which since this is gen V, you can slap an eviolite on.
Early Headbutt from Bagon is also going to help it have consistent early game damage. The main thing you're looking for in game is the balance of Pokemon you like and teams that can move through battles at a pace that let's you have fun and not lose too much momentum.
That being said, I'd probably give the same advice for any game they both appear in when looking at them as early additions.