The only correct answer regarding things to absolutely have is
microtransactions. Add as many interactions requiring microtransactions as possible -level ups, acquiring TMs, entering special areas, bike usage-, and I can assure you that will keep people
literally invested on the game.
Given it's an MMO I'd expect lively exploration: Pokémon should be able to use various techniques to interact with their environment and help the Trainer reach to places. Vine Whip or Tailwind to cross a wide chasm, Ember to light up the candles in the haunted mansion -no, not Flamethrower, or you'll make the curtains and the rest of the place go down in fire!), Icy Wind or Ice Beam to freeze small bodies of water into walkable platforms, that kind of things.
Battle-wise, as much as it'd be realtime I'd only be interested if it keeps enough of a sense of turn-based so as to actually be able to sit back and enjoy
thinking about the battle. So, either implementing a passive Defend system or some other elements that counterbalance the need to Act Now!.
Implementing AoE healing might be a must, there things like Reflect, Barrier and Safeguard I guess can help a bit. And of course, positional and geo effects facets for the battle engine, such as projectile attacks taking into effect wind and drag or be subject to the altitude of the target so as to make aiming for opponents more interesting.
