~Them being "Basic" Pokemon and not having to be evolved in to means they are absurdly easy to get on the board. (Yes, I know some GX need to be evolved in to and Mega Evolutions end your turn, if you do not have a spirit-link) Having such powerful pokemon negate the evolution system really defeats a core aspect of the game.
~Most of them have energy costs of 2-3, for fairly powerful (enough to one-shot most "regular" pokemon, in the early game) attacks.
~High HP counts means "regular" pokemon have a fair degree of difficulty defeating them. Yes, you get two prize cards for beating them, but you will be losing 2-3 pokemon to defeat one EX or GX. So the two prize cards you get for defeating an EX/GX is not really much consolation.
~No restrictions on deck building leads to decks filled with these pokemon (at least in MTG their "Legendary" cards are limited to one in play per card, for example)
~Min-maxing pokemon-trainer/energy cards means much higher chances of drawing them at the start of the game (or taking mulligans until you get one)
I wish I had a list of ideas on how to approach this situation, beyond "Get this specific list of cards and never play decks you want to play. Or stop playing, you big loser-whiner!" but I know the community is just going to ******* me for making this post but I still feel like EX/GX are a cash-grab/excessive power-creep that makes the game un-fun.
I wish I had real friends I could play the game with so we could play friendly games and have a few 'house rules' about including horse ******* one's deck.