I've got an up-to-date cube (all the way up to Guardians Rising!) that has some EXes in it; it's an unlimited cube though, so it's not strictly modern or expanded. (I much prefer it this way, too - a lot of my sensibilities are grounded in gen 4, and there's some great cards from then in here.) EXes are a huge problem. Firstly, with power creep, even regular gen 5/6 mons are more efficient than previous gens. Secondly, even in current gens, most stage 1s and pretty much all stage 2s *suck*. You can't beat the utility of a basic. And thirdly, even without those two factors, the higher HP makes for a huge challenge. A lot of otherwise great cards max out at 70 damage; that's a 3HKO on even the shitty EXes.
So I've omitted them from my cube entirely, save for the miniature ones like Manaphy, Victini, any Shaymin, etcetera. They're actually all wonderfully balanced. Huge utility and decent but not OP statlines for basics, yet the 2 prize rule makes running them a 50/50 decision. It's great, and it gives stage 2s a chance to shine.
It's still early days for my cube testing. 600 cards is a lot of room for new "broken" stuff to be discovered. I'm a little unsure about some of my specific stage 2s, and Grass could be a problem later since Vileplume is scary with FoGP/Broken Time Space and Aether Paradise messes hugely with the much smaller damage numbers hit in the cube. Time will tell!