For the Secret Rare. It's definitely not worth putting in Fire Energy just for him. His best purpose is for getting the donk on Gible, Swablu, Tynamo and the occasional Dragon Deino. But you already have a good match-up against Garchomp (Unless you run Rayquaza EX), and the Dark Deino is used more then the Dragon one (At least that's what I've heard). The Tynamo donk is very helpful though. But if you're already running Rayquaza EX and Fire Energy, I'd say he's a good idea. He's a good attacker against Garchomp and Rayquaza EX (As well as most other Dragon types) if you have Fire Energy, because of there Dragon weakness. But sadly, he's not very good in most other match-ups, since his attacks are fairly weak, and most things basic forms have to much HP too be donked be him.
For the EX. In my opinion, putting him in as a 1-off tech is a bad idea. Since he's not the easiest to set-up in one turn as a surprise attack. And if you want to attack with him consistently you'll need a lot of Switch or just have to use him every other turn. Also, having 3 to 5 Fire Energy just for a tech seems like a waist. I think you should run 3 or maybe 2 just so you can attack with him consistently.
As for when you're attacking with 2 or 3, in my testing, it's a little slow. Having to get out 2 or 3 Eels plus 2 Rayquaza EXs with Fire Energy takes a while. But when it does get going, it steamrolls EXs like that (*Snaps finger). I haven't tested much against decks without EXs (Just by coincidence of my friends not playing very many) but I'd assume you'd just want to focus on using another attacker. If he's good in a match-up, focus on setting him up. If he's bad in a match-up, don't bother. However, since it has a weakness to Dragon and is an EX. being weak to Garchomp and Hydreigon makes it completely unplayable... Oh, wait. NO IT DOESN'T! While yes, that is a flaw, you can use other attackers in those match-ups.
As for which one I like more. I prefer the EX. The SR doesn't do enough damage to hold itself after the first turn. The EX has it's flaws, but it's ability to KO anything for just one attack is definitely useful.
~MtC