Really I think it's not so much that EX Pokémon like Charizard EX exist in the first place, it's the fact that since the reintroduction of EX Pokémon during the BW era they have all been basics, even if they shouldn't have been. If they had taken the same approach they did during the original (RSE) EX era and made them what they were (ie stage 1 or stage 2) they would be less annoying...but that takes us back to my first point about evolution in the format(s).
I was around for the original Pokémon-EX. Having Pokémon-ex as Evolutions was as annoying as having them as Basics. Perhaps worse; the designers tried to balance out the Stages at the time by giving better attributes (such as HP) or effects (attacks or Poké-Bodies/Poké-Powers) to Evolutions, but instead of balance it just made being a non-Evolving Basic a dead end.
As it stands though I don't see how anything can really change. The only thing they could do is stop making mega Pokémon until the current format rotates out and then go with the theoretical new mechanic. And that won't happen. Combine it with the fact that EX stuff sells; both to the younger players who will pretty much do whatever they can to get any of that stuff and to the players that can afford and are willing to spend to get the stuff.
I have considered this and the problem isn't the existence of Mega Evolutions, the problem is how fast and strong they have made them. While again not easy, I propose raising HP scores while damage output remains the same or (preferably) drops a little. This would create sets that could still compete with what is current (because I am talking
significantly higher HP scores, also preferably going back to +X for Weakness). Eventually our contemporary cards would rotate out. This ties into my earlier suggested guidelines.
...and vice versa as long as the game continues to sell at a profitable rate.
I think the changes you proposed could work if implemented correctly. I also think the EX designation should be limited to legendary/mythical. An investor may not see it as such, nor may a highly competitive player, as it risks changing the core gameplay that currently sells into something that does not.
As a reminder, if this TCG was purely about profits and short term thinking, the TCG would be dumped on the market a la the Digimon TCGs and others. The powers-that-be would have to periodically "reset" because kids would get tired, it would stop selling so distributors would stop buying, but you save on costs for Organized Play, Research & Development, etc. Having the kind of Organized Play that we enjoy seems to stabilize the game and keep it chugging along (in the U.S. the Pokémon TCG made its full debut in 1999, over 16 years ago!).
It is important to remember as well that while normally the largest target demographic would dictate the direction of the product, there are special circumstances here. Most people that buy Pokémon TCG boosters appear to be those just getting it as a (comparatively) inexpensive Pokémon product: they neither play nor collect in the proper sense. Actual collectors do need to be considered, but in the end it is the card game player who has needs that can be meet without alienating the other two groups; in fact largely without affecting them. So for maximum profit yield while maintaining a product they can be proud of with a self-sustaining customer base, there is a legitimate argument for making this the best game it can be, where people can enjoy using any of their favorites in at least somewhat competitive play.
Player turnover is a huge thing; plenty of people that played it as tweens and teens now are having kids that began playing. Here is the thing; a lot of people left because the game has been in decline for the reasons I mentioned. Not the only reason people leave, but one the-powers-that-be can control. I've gone from a fanboy that would semi-regularly explain how the Pokémon TCG was a great hobby that can teach kids how to trade, a little business sense and give them a shot at winning scholarships via competitive play (
on top of being a fun, family hobby) to discouraging people from pursuing it. If things keep up, I may have to actively warn people away as this game has gone disturbing places lately. More and more the designers seem to be pushing to make this game about one-sided dominance, not a back-and-forth duel.