In my personal Opinion, I like EX's way more. They have More HP, Can Be Candied, and you can run a 4-4-3-2 line of an EX with NM/Holon Farmer.
Though EX's have many high points, they also have low points, such as 2 prize cards are taken with a KO, have dual weakness, and there are many Anti EX's.
EX's in my oppinion are high risk, high return. Lv.X are great, and don't (yet) have a counter (by that I meen there is no card that says "prevent all effects of attacks from pokemon LV.X", or "This attack does 20 more damage if the defending pokemon is a Lv.X")
I like EX's Better though.