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Here's what I would do if given the powah.
Region
>set it in a more original land instead of basing it on a real location.
>combine aspects of real world cultures into something unique a la Pathologic.
>cohesive theme like solemn mountains, tropical, instead of fire area, water area, snow area, desert, etc.
Pokemon
>instead of HMs, make them like a key item and any Pokemon that can learn that move can automatically use that HM. Some Fire Red romhacks apparently do this
>use design styles often in gens 1-4, less cartoony or stylized Pokemon, more that have rugged, realistic, organic forms. Obviously some exceptions for machine Pokemon and others.
>pic related are the final forms of starters
>more version exclusive mons to encourage trading
Legends
>dual legends relevant to the region, not the universe
>barely make a showing or talked about until after the 7th or 8th gym, no world saving plot point
>have a postgame trio to find, some elaborate puzzle shit like Regis
>some mythicals that are deep, deep in the wilds and hard to find
Routes/Towns/Gyms
>all routes aside from well-travelled roads are labyrinthine and have lots of secret nooks
>bring in grottos from BW2
>caves vary from small to expansive and you can easily get lost. Flash effectively mandatory
>every town has a Pokemart aside from a rustic town using a farmer's market with unique items. Think Slateport.
>Secret Bases a la ORAS
>Strength puzzles and ice slide puzzles common
Gameplay/Visuals
>upscaled and improved models from Colosseum/XD, particularly the move VFX/SFX
>tile based overworld with no diagonal movement
>if not the above than tween sprites a la Gen 5 with 2.5D Octopath look
>rebalance Fairy Type, change Dragon immunity to resistance
>make Ice super effective against Rock, maybe some other buffs
>general rebalancing to shitty moves
Also, no focus on story or plot. Linear progression across the region but very little handholding.
Can't think of much else, but it's a start.