Collectible card game AI for a game to make it just like real life is horrific to try to program things for on a supercomputer, doing anything in real (ish) time on the GBA's 16.78MHz ARM7 with just under 300KB of memory and all of 32 megabytes of storage space is just not possible. The reasons why would involve me going into some depth on how games work, consider it this way though there are 32 pieces on a chess board, each can maybe make an average of 6 possible moves and thus trying to predict any number of moves ahead like a human might then means you are very quickly dealing with exponential numbers and having to crunch the lot or at least something close to it. I had the dubious pleasure of reading up on the rules to the game earlier today and it seems the pokemon TCG has however many possible cards, various win/loss states, effects that do all sorts of things, weaknesses, probabilities changing damage*, trainer cards, retreats -- at any given point there are a serious potential amount of moves available (easily in the thousands per turn) and all way way way beyond any supercomputer today.
*to be fair most of those seem to be "flip a coin, heads you win, tails I lose" so 20 plus 20 if coin in your favour can probably be safely approximated to 30.
To help with this the developers sharply limit the options, cards available to them and their opponent and maybe add the results of a few player matches and strategies that work against and with a given deck, depending upon the game they may even have a limited version of xray glasses. If you want to go a bit more in depth then the Magic the gathering people have a good article from when they made their XBLA game (and the 360 is order of magnitude more powerful than the GBA), http://archive.wizards.com/Magic/magazine/article.aspx?x=mtg/daily/feature/44
Now it may be that the devs just use a basic heuristic or 5 to try to make an AI that kind of works, pokemon TCG and similar games like yugioh are often quite broken to the point where this is possible (it is the collectible/rare part of the cart game thing and why you end up with a long list of tournament rules against certain combos), but I would be shocked if it was solely that. You alter just a couple of cards and you alter all kinds of probabilities, counter strategies and more that the devs would be counting on for the deck and then things start breaking down very quickly.