Ooooh geez where do I
start... I mean the question of what do I want in a Pokémon hackgame is basically exactly the same as what do I want in a normal Pokémon game, plusminus technical capabilities.
So... let's start with the obvious.
Obviously, the story. Romhacks in particular use the same engine and most of the same assets than the normal games they originate from, so the first element that greatly distinguishes them from the competition and that it's very easy to add innovation for is the storyline.
On other things...
- I support AI3X in having everything decapitalized. We're not in 1999 anymore.
- If possible, wider datasets and datatypes for Pokémon items and moves, in particular when it comes to the names. Again, we're not in 1999 anymore so we shouldn't have stuff like "PRZCureBerry" or having a "Normal Ball" and also a "CamelCaseBall". 18-20 characters limit for item names and location names should be a fairy sensible amount.
- It's more or less standard feature by now, but some oldish features like Physical/Special split should be a given. Ditto replacing trade-requiring evolutions. Fairy type? Why not.
- Substitute HMs for a different kind of overworld moves engine. I'd say try something like Golden Sun's, where there's a lot of ways to interact with the environment and those moves are designated by the job class / species / something and don't take room in the battle moveset. Give many moves ability to cause interaction. Vine Whip to cross a chasm? Ember to light up torches when you don't have Flash available?
- More doubles / triples / tag battles, depending on what the engine supports.
- The ability to choose from more than one starter set at the beginning of the story. Presumably the rival's choice would depend on your same set, too.
- Speaking of rivals and stuff, make those kinds of opponents autoleveling, so that they remain a fair challenge to the player no matter what level you are at.
- While following Pokémon is not a needed thing, if you're gonna have it please make people react to them, in particular if the mon following you is a rare Pokémon, a revered creature in your setting's myth, or one with world-rending powers.
- Have a concept of missions or arcs that is followed in-game by some sort of journal, kinda like what FR/LG had, so that we can always know where we were or have a clue of what we are supposed to be doing.
- Depending on what the art dept. is up to, cutscenes. But not of the pathetic current trend of "interrupt the current gameplay" or "press X to lift a finger" thing (aka "not a videogame but an interactive movie"); rather be it story / expository cutscenes at the beginning or end of each arc, kinda like the Ninja Gaiden games.
- Make more of the world map available from the start in general terms, but not all of it - of course, getting to the best stuff would require learning particular moves or acquiring particular items.
- if we're gonna have Legendaries make fighting them be a Worth It™ experience. Nowadays players are so well-prepared (and they soft-reset, too) that fighting a Legendary is just a glorified normal Rattata encounter with different music thrown into it. It should have more oomph to it, like with Final Fantasy special bosses. A roar, a woosh, and then you get into a special scene where it's two or three (depending on the engine) Pokémon against the legendary beast at once, and he gets the HP bar and the moves adjusted to compete against the combined might of your team. Like, having dual turn or different engage modes each with its own HP bar. And if it is possible to implement special mechanics, even the better.
- Have a wider selection of Pokéball types available early in the game.
- if the romhack is to have Gym Leaders and Elite Fours, make them not be transparent or useless in the story.
- If working the romhack on G4, be careful with the save/load times :p
- If possible to code it, remove the useless wait time between battle animations (say, losing HP from poison) and their slow ass-messages ("D'uh, you lose HP from the poison"). Again, 21st century stuff.
- Throw lighthearted jabs at previous generations. "Cooltrainer" type, eternal save times, sludges that transform people when eaten, D/P's memetic translations, "your mom had a bad egg", all is fair game.
Also this:
One of my greatest grips with the latest two generations is that all trashcans are empty.