Not only were the computer players' decks on TCG-GB horrid, but the game itself was extremely glitched, and that may be putting it nicely. The coin was always weighted at almost 60-40 in your favor, whatever "in your favor" was, and that was probably one of the more minor glitches.
Definitely, if a new electronic version of the TCG were to be released, it would have to be done a lot better than the GB version was. For one, the cards themselves are a lot more complicated than they were back then, and nothing kills an electronic version of a TCG faster than blatant rulings errors. For another, as was mentioned, the computer players would need far better decks. I could understand if the decks of some of the lower-level computer players were a bit noobish, but once you get to players that you actually have to win a few battles to get to, you shouldn't be able to beat them lickety-split.
One feature that I, for one, would love to see, though I would be extremely surprised if it were actually done, would be a built-in card creation engine. What do I mean by that? Basically, the ability to build cards of your own design into the game without a cheat device. Why would I be surprised if it were adopted? One, allowing the AI to adapt to user-created cards would take some very good programming. Two, it would be all but impossible to make sure that a player couldn't create a truly broken card with this engine, even if it had built-in card creation rules. Three, it's a matter of vanity -- would Nintendo really want players to be creating their own cards, quite possibly ones better than the professionals could make?