It doesn't provide a defense against them, it just speeds up the pace of Evolving... which unless it was worded otherwise, also applies to some Pokémon-EX (Mega Evolutions and whatever they cook up later).
Pokémon-EX are not broken as a mechanic; you get a Pokémon that usually has higher-than-normal HP for whatever Pokémon it is and may get an Ability, Ancient Trait and/or attack that also is better than normal for all that is involved but at the cost of:
An important thing is that those last two really shouldn't have been necessary because seriously, giving up an additional Prizes should have been enough. In fact it does matter: there have been a lot of Pokémon-EX which have been under powered and either seldom used or only useful for a very short time. There are many non-Pokémon-EX Basic, Stage 1 and Stage 2 cards that are far more abusively powerful than these Pokémon-EX. The real problem is, in a word pacing: the game is literally being pushed to run faster than its mechanics were designed to allow it to run.
- Being worth an additional Prize when KOed
- Being the target of certain counter cards already in the environment
- Being unable to access certain pieces of the support
The pacing issues would be made worse by a card like Broken Time-Space returning... which we are already seeing with Forest of Giant Plants: Expanded gets what I hope was an accidental First Turn Win deck and I fear I was far too dismissive of Giratina-EX (ANO) and Vileplume (ANO) decks... in large part because I forgot they can attempt to spam Shaymin-EX (ROS). Oh look, tying things all together again: Shaymin-EX. For the record on the PTCGO (only place where I play) I not only have but have had four for a while (made it a priority). I even managed to pull a lucky Full Art version from a trade locked pack one of the first few such boosters I got, so it isn't a matter of being "jealous" or lacking the card. Ability based draw allows some stupid fast set-ups right now and enables a lot of combos that frankly suck the fun out of being the opponent. Contrary to popular belief, losing isn't supposed to be 100% awful; it is just supposed to be "less fun" than winning. You're not supposed to play the game just because you've got a chance at winning, but because you enjoy playing.
Well, that is how I'd put it, anyway.
Addendum: I won't post it right now because long post is long, but I have a great example of how important it is to apportion "blame" for imbalance and pacing issues in a format... and it involves Base Set through Fossil.
Pokemon-EX are not broken as a mechanic, but they are broken due to their implementation into the TCG. Although we've had AMAZING stage-2 cards recently (Empoleon, Shiftry FLF, Blaziken FFI, Blaziken PCL, Garchomp DRX), none of them have seen major tournament success, except for Empoleon. Why is this?
I recently played against a FluffyChomp deck in Expanded with an Yveltal list. I won handily. Why was that? It was a lot easier for me to load a 170 HP Basic with a Dark and a DCE to just start taking potshots at his board than for him to load up a Stage 2 with a Fighting and a Water energy each, a Silver Bangle, and two Stage 1s on the bench. Granted, he had Gabite's Dragon Call to stream Dragons, but I was able to kill it quickly. He did get 150 damage onto an Yveltal-EX with a Garchomp, but I was able to retreat and power up a 3 energy Yveltal-EX in a single turn.
If the EXs were to have much worse attacks, I would be comfortable with them (see Blastoise-EX and Venusaur-EX). However, that is unfortunately not the case, with the ability to do things like 30 and 1 sided item lock for [C][C], 120 damage for [L][C], 90 damage with 30 snipe for [D][D][C]. Worst of all, all of these cards have really good support.