I agree that them abandoning mechanics after a few sets is bad, but M Pokemon-EX were not one of those mechanics. They lasted the entirity of the XY era. That's just as long as things like Pokemon Lv.X did. Having a mechanic be unique to a specific era that spans like a dozen sets is perfectly acceptable to me. But yeah, mid-generation things like Ancient Traits and Pokemon LEGEND were disappointing. (Technically I guess the HGSS block was its own "era", but it was so short I don't view it in the same way as, say, DPP or XY. I similarly don't view the 3 e-card sets as a unique entity.)
I don't think an average of 4 unique Megas per set was realistic, especially after Pokemon BREAK were introduced. Yeah, a couple of XY sets did have 4, but they had much larger numbers of UR's than average in general as well. Again, realistically, the fact Megas take up 2 slots was the issue. Short of making their base forms not UR's, increasing the number of UR's per set or releasing an ungodly number of products with multiple promo EX's (which, knowing Pokemon, would be ridiculously priced anyway), there was nothing they could do IMO.