I'd advise learn to use a programming language (steep learning curve) or pick up all the tools and do a romhack.
Advice would be Java or C++.
Or hack the GBA Games if you don't want to do it from scratch.
Either way, make something ~Good~
As for features We haven't seen, here are features I think would rock.
Different types of battles (different rules) > such as multiple pokemon at once, a real time battle system, like Legend of Mana, but with your Pokemon, A battle system with pokemon like in final fantasy tactics. Possibly to option to CHOOSE what kind of battle every time, or have it be random.
Pokemon Appearance customization: pick from a selection of heads bodies, etc. basically choose your pokemon's pose.
Pokemon Equipment: Get Pikachu a pair of matrix sunglasses to make him looks sweet, Pokemon Body Armor, etc. Make the scaling reasonable. No Knife should do more damage than a sword, if you add weapons, thats just absurd.
Minigames: Make alot of minigame type activities like the pikachu surfing. Make them frequent. Possibly as....
Quests: Do try to avoid lots of delivery quests, they just suck. Try to come up with more than just "take this person X", find "X", find "5 X", and defeat 15 X. Those are unoriginal and boring. Hence Minigames. The Jak and Daxter Series illustrate a good implementation of quests. WoW illustrates bad, and repetitive, quests.
Maybe an Original Plot.
The Ability to catch ALL of the Pokemon, in ONE GAME! GASP!
umm.
Here's one that would rock, but would be outside your ability at the moment. > Allow the game to export saves for the existing GB, GBC, GBA, GBDS Games.
IE, Go to Kanto, Go to a Pokemon Centre, Go to the Computer, choose export, and it'll make you a gold/silver, red/blue/green, and firered/leafgreen save on your computer with your current character and his pokemon (the ones that are in those games, with available moves.)
This feature would be cool, but hard to do.
Multiplayer over the internet. Possibly just Battling, Possibly MMONess.