There's not that problem this time around. The DS, which seems to be designed with this in mind, has a slot for GameBoy Advance games, while you can play them - it does do more interesting things for your DS game.
Yes you can trade, however, there is certain catches:
6 Pokemon a day per cart. After you've gotten the National Dex.
Getting the National Dex isn't too hard. You have to catch the trio of legendary Pokemon, Azelf, Uxie and Mesprit, or do what I did and trade with a friend. The rest of the Pokemon can be seen by battling trainers, Palkia/Diagla which can be seen in a picture from the Village Elder in Celestic Town once the Elite Four have been beaten.
After you have the Dex, travel trough route 219 (Under Sandgem) to the PalPark where Professor Oak will great you on your first visit and give you a new feature for the Poketch. Now comes the fun part, talk to the man at the desk who will tell you about the "Catching Show".
You may now send your Pokemon over.
To do so, reset the game and if you have a Pokemon GBA cart inserted you will see a new option come up: "Migrate from Emerald/Fire Red/Leaf Green/Sapphire/Ruby." Select it and you will be shown a box screen of your Pokemon in your PC in said games.
While transferring, you have to remember a few things:
No Pokemon with a HM attack can be sent; you'll have to get the Move Deleter either in Fuchsia City or Lilycove.
It's not a trade, it's a transfer, meaning only the Pokemon from RSEFLG cart are being sent, and you're not sending Pokemon back.
It's a permanent transfer, Pokemon cannot be sent back. However, if you're feeling devious the Emerald clone trick is for you.
Once you have entered your Pokemon, go to Palpark and you will be entered for the Catching Show. You might think it looks a little like the Safari Zone, indeed it does. There are several places, (forest, plain, mountain, sea, lake) that your transferred Pokemon will be hiding in, they can be found in what area they are most likely to be associated with - For example, Regirock will be found on the mountain area, while Mantine will be found in the sea. The rarer the Pokemon however, the more time it takes it to show up, but don't threat, it's easy to catch them. When you come across them, it's simply a case of throwing the ball, no mess, no worry, you'll have it quickly.
After you've caught your six Pokemon, the guy will call you back and give you a berry depending on what your score is. Fun wasn't it? You'll have the option of sending your Pokemon back in to the park, or keeping them in your box.
However, you won't be able to transfer Pokemon from that gamepak for a full day, (24 hours). But you can transfer from other gamepaks. You also won't be able to transfer if there are still Pokemon in the Palpark that you haven't caught. Even with its different approach, the Pokemon you've caught are treated if you got in a trade, Sam IT/OT of the Gamepak of which it came from, same EVS/IVS and even if it was holding an item prior to transfer, they even get bonus EXP in battle.
So yes, you can stop crying now.
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