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I usually catch the remaining legendaries and finish as much of the pokedex as I can before the next game. I also level up my team of my favorite pokemon (at the time).
Usually, my brother (yes, it's my brother who owns the HG game) would ( if our DS wasn't broken) to SR for shiny legendaries. So far, he caught a Shiny Ho-Oh. Other than that, I don't know.
I train my team to level 100, complete my Pokedex, and breed more Pokemon and train those. I also begin to focus more on special collections (e.g., shinies, Pokemon with great egg moves and perfect stats, etc.). If a game has a battle frontier in it, I do that, too. Somehow, I find that Pokemon games can never really be "finished."
After I beat the story line, I try to fill up my Pokedex as best as I can, because currently I don't have the money to go re-buy the old games, nor the time to beat them again for that matter, so I really I'm stuck with HeartGold and others willing to trade with me to fill my Pokedex. (I also have a DSi XL so I really can't even transfer them over... unless I can manage to find my old DS Lite)
I also try my best to train all my Pokemon up to Level 100 - I take pride in that when I accomplish that!
I love going back in the games, rebeating the Pokemon League, then since there is the whole pictures things now I try to find Cameron as many times for pictures. I also beat the Pokeathalon as many times as possible.
I really don't like starting games over, it just erases all the hard-spent time you've put into that game. But that's just my opinion.
So after beating every single trainer in the game, winning pokeathlon, finishing johto dex, and 400 hours gameplay, I hit myself in the head. I went down into union cave where lapras is, and I HAD NEVER BEEN THERE. The trainers? I didn't battle them. I can't believe I had never been down there, having the game since the release date.
For me, I make sure I truly am the best in-game and battle out until I'm the winner of every competition etc, fill out the national dex, and then simply wait for the next game to come out so I can transfer my favorites and do it all over again ^_^
After beating the game, I usually evolve any Pokemon that I haven't found in my Dex yet.
Or Amulet Coin on highest level Pokemon and continuously fight the Elite Four
After I beat the elite 4 and push Red off the mountain, I usually start breeding for good natures and IV's. When I don't do that, I send important pokemon to my platinum, and then restart.
I wouldn't consider it as beating the "entire game", after beating the Elite Four, because after beating the Elite Four you can go to the Battle Frontier and take on some pretty good challenges. Well Technically it "is" beating the game because it says THE END after beating the Elite Four but I don't consider it as beating the game. But anyways, after I beat the Elite Four, I go and catch and then breed as many different pokemon as I can, and work my Togepi up and evolve it into a Togekiss. I also go for Event Pokemon and legendaries.
like Pan does collect all pokemon but I have a mate who just recently completed pokemon with 493 in pokedex lol and he helps me lol but he has got 715 hours gameplay time on so it has took him a long time to complete it lol :)