Don't be afraid to go outside the box, try to avoid cookie cutter concepts
Everyone knows certain things about pretty much every Pokemon game. You start the game, talk to a professor, pick a fire, water, or grass pokemon. Fight 8 (or 18) Gym leaders fight an evil organization defeat the Elite 4 and the rest is just fleshing it out. Some of these same old tactics can grow tiresome to the more experienced pokemon players. So long as you take the time and effort to think things over you'll be able to come up with different unique concepts. The thing that drew me to Reborn watching shofu's LP Episode 1 in the first place was that EVERY starter was made available from the get go. 'THIS IS SO NEAT, look at all the choices I can make and WOW'. Try and find places where you can make changes to the way things work, replace the professor with some other profession for the role that will serve the same purpose. Maybe make the starters not FWG. All in all just take some steps to differentiate your game from the same old same old. One of the best examples I can think of when it comes to Reborn in this regard nowadays would be the dreaded field effects. It adds a unique interesting dynamic that individualizes it from other games. Some of the inspired fan games around here have followed suit because it was a good idea, something Reborn is ultimately remembered for. If you make your game like everyone else, I will likely forget it like everyone else.
P.S. While I wasn't too fond of Snakewood, I'll certainly remember it, and many others will as well.
Be original, be different Be the one that stand up and shocks this system