>>46679092I can give you 3.
1. Being tied to a hold item while only being able to use 1 Mega per battle means certain forms never saw the light of the day. By ORAS the internal power creep was already so severe that by VGC16 only 3-4 out of 50 available forms were actually worth using on a competitive level.
2. Building teams without a Mega evolution was not optimal so you were pidgeonholed into dedicating one team slot to a curated list of 50 GameFreak-approved favorites if you wanted to remain competitive (in practice much less since majority of Megas were useless, as mentioned before).
3. Kalos Pokémon became marginalized in their own gen since all the focus was on Mega evolutions and all but 1 Kalos Pokémon never got a Mega. To this date people call it one of the most forgettable gens of all time.
All in all the lack of quality control ruined this mechanic by the time a second (and last) batch of Megas was introduced into the game. It was easier to drop the mechanic altogether rather than redesign the whole thing from ground up.
