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inthis situation i say whatever floats your boat, seeign in game maker, sphere and the rpgmaker series you can makla decent pokemon game in all of them so, it is up to you and what you are willing to learn
The best program for making Pokemon games is Sphere, but it also has a high level of difficulty. Making a Pokemon game in Game Maker would be a huge drag because of the poor map editor it has.
The RM series would be the easiest to make a Pokemon game in, just take your pick between RM2K3 and RMXP really.
RPG Maker 2003 Is the easiest, but for the best i recommend RPG Maker XP or Sphere, If you have the time to learn RGSS or JavaScript than get the last two, you get much more possibilities with them!