While i agree on the matter of mega evolution not being used for the full party, as far as i've seen in anime, it has only been used once per party if i'm not mistaken, maybe the mega bracelet can only react once with a singular stone per battle, which is why i didn't mind that "issue"...
Another thing is i DID mention that the fact that they're all one item duplicated would take the "adventure" aspect away, this is why i suggested what the author of gaia did, secret places to explore and obtain the mega gems, maybe he could even make it so that you need to battle the same pokemon you want to mega evolve before doing it, as seen in the anime with lucario's mega stone.
On the other hand, putting stones in places that require dive could also be fun, like you have to use all of your HMs in order to obtain the mega gems, one thing i would hope is for (as you said if i'm not confused, its good anyway) having to obtain certain badges to use the stones in the first place, while not all of them, maybe the first 4 badges of the second region ? (that is if he's planning on doing something like Kanto and Jhoto with all 16 gyms)
On the topic of gyms, i thought of a weird yet funny idea, why not put wild encounters of the pokemon the gym members use inside of the gym itself ? like walking in the graveyard and finding a Gastly or something, would be more motivating to get the badges...
OR Just drop that idea xD, sounds stupid maybe, anyway, just give the elite 4 mega evolution once you clear the first region for the first try, just to make it harder to battle them a second time...
And please, give all the pokecenters/important places fly locations, it'd REALLY be helpful...
anyway! those are my dumb suggestions, have a good day everyone !