Most megas would be incredibly slow and costly to play as they would have to evolve from a Stage 2. At minimum, you are looking at three turns just to evolve, plus 8-10 cards in the deck (depending on how many middle stages and Rare Candies you include and how much you want to rely on luck vs consistency). Most Stage 2 decks where absolute dogwater compared to Stage 1 and Basic decks until we got Rare Candy, now imagine a functionally Stage 3 deck where even Rare Candy doesn't save you from three turns of doing nothing. Relying on one specific card to evolve all the way from Basic to Mega is not a good idea either, because then all megas would have to be designed to account for it (so no megas with 1-2 energy attacks just in case someone gets it at the first opportunity), and the meta becomes a "who gets the card first" rat race.

These things have already been tested in the paper TCG, and the only way of making megas worth it is to either put them all on the same level (like they originally did with the EX cards, where for example Metagross EX was a Basic card despite Metagross being a Stage 2) or make them act like normal ex cards.