KEEP old features that people like. This includes a battle frontier, contests, battle tents, Pokemon Amie, Super Training, DexNav, and a way to rechallenge fought trainers.
Replace secret bases with a "Virtual Room" that can be accessed any time. It operates like a secret base, but is much more customizable. In addition to placing trainers in your room, you can also make it possible for guests to catch a limited selection of wild Pokemon in there as well, which the room's designer must've already caught in-game.
Give the player a portable PC (like, a smartphone item), with which they can toggle their party at any point in the overworld. Disabled at the Elite Four / Battle Frontier.
Expand the number and types of ridable Pokemon, and make riding an at-will thing. Fast rides can jump over ledges, steady ones can travel over harsh terrain and smash obstacles, swimming ones are self-explanatory, and all flying Pokemon operate like ORAS Latia/os.
Make gyms no longer restricted to a single Pokemon type. Instead, have them based on environments and themes, like water, deserts, urban areas, mountains, etc.
The Elite Four are now based on different battle strategies/formats (sweeping, walling/traps, doubles, etc.) and have whatever Pokemon they need at their disposal. The Champion's team is simply well I diversified as has high IVs/levels.
Vastly expand the number of optional sidequests in the game, making it obvious in the overworld who offers them (like a special icon over their heads). This can range from simple fetch quests and catching/defeating certain Pokemon or more complicated tasks like a trading chains. Rewards can be monetary or material or can be exclusive or rarer Pokemon offered earlier in the game. A good deal of longer sidequests constitute some of the post game content.
Keep existing megas, but only give new ones to third evolutions, Pokemon that last evolved with an item / in a trade, or legendaries. Give Pokemon that need them real evolutions.
