>>51113326A. Retcon megas into being straight evolutions for the few weak Pokemon that got them, then make some more. Forget all the OP ones ever existed.
B. Bring back the Pokemon Refresh mechanic and the friendship meter. If you max out the meter on a Pokemon, it unlocks a hidden boost that gives the Pokemon a buff if fighting something way stronger.
C. An "equipment" slot alongside the held item slot. There's a wide variety of equipment you can use, and each Pokemon is allowed to equip some of them, but not all. Traditionally weak Pokemon have access to a much wider variety of equipment, whereas strong ones might only get the weak stuff like a shirt that increases attack by two points.
D. Make Eviolites, Everstones and some other held items into a toggle that you speak to some lab NPC to activate, some big fancy machine they zap your Pokemon with. Weaker Pokemon can toggle more effects at once, while fully-evolved, 500BST mons might only have one toggle and no selection to use it on.