I think overall, SR is better because it can donk, uses Lightning to do so, and only give up one Prize. It's easily techable into Eels and Garchomp. Rayquaza EX is a good card, but even though it can one shot any card in the format, it lacks the support it needs to do so. You need to discard 4 Energy to knock out an EX with Eviolite. (except Dragons) Doing that consistently will be difficult, especially with your Weakness to Dragon. A Darkrai two shots you and three shots your Eels, and Giratina can one shot a Rayquaza with Shred, both of which can be played in Hydreigon. Hydreigon one shots you. Garchomp one shots you with either 2 Altarias or using it's second attack. Other Quaza EXs can one shot you with 2 Energy. Quaza SR can one shot you with Shred. Zekrom two shots you with Bolt Strike. They also one shot your Eels with those same attacks. EX also requires two Energy types to deal damage. While SR uses two types as well, it's main purpose is to donk, not kill EXs.