Well the first thing to do is find a good base for your idea. By this I mean you need to create a goal (in this case make a game), then you need to motivate yourself to achieve this goal. (This is usually done by posting on the forum for feedback, talking to friends, and praising/critiquing your own progress) Afterwards you either want to take Poeman's advice and make your own engine, or use a game making software already out there such as RPG Maker XP, Rpg Maker VX, or Game Maker. After you have a goal in mind and something to begin working on your goals you could either find a frame to place on your base (ie: Poccils starter kit if you're using RMXP) or type up your own scripts to use. (In RMXP, you would use RGSS, a sublanguage of RUBY). After you have a real base you need to make sure you understand it. There's no point in tryng to script something that's written in a totally different language. After you have a basic grasp of what you can do with scripts you should start developing your ideas. Try to break out of standard PokéMon Realms. Remember though, this is just the basic development stage. After this, you should start making the real decisions that matter. The region itself, the starter choices, the plot line. The things that are less likely to change in the end; make those decisions. Afterwards, you should go back and edit the story or any development that may contradict. For example, if you chose in the end for your region to have a tropical feel, why would there be a snow covered starter town. (minus any form of odd weather occurences) After all these things are done you might want to, if you already haven't started, visualizing the creation. Try to visualize how you want the areas to look like. Visualize how the gym leaders look, visualize what music would fit best with which towns. This step really matters. The next step and my final piece of advice for you is to begin locating your resources. If you want your maps to be in 4th gen, find a 4th gen tileset. If you think the HP boxes should resemble platinums, go on the spriters resource and get them. Collect music, or make/edit some with a program like anvil. After all of this is done, you should be well on your way to making a game.
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Was that helpful?(or cheesy.. I especially like sounding cheesy...<3) o-o