Apparently, I was wrong about a TAS of the second game being faster than the first. There's already a TAS of Pokemon Card GB2 on nicovideo by cstrakm and it's considerably longer:
http://www.nicovideo.jp/watch/sm7256179
I never played this game and know nothing of Japanese, but from what I read, you need to have all legendary cards before entering the final stage. They can be gotten by challenging the Grand Masters once they're rescued, but he uses a faster alternate method to get them sooner.
This also allows to get Legendary Zapdos, whose pokepower can get rid of benched pokemon and deal damage to things that can't be OHKO'd. I could see that there's a trainer card able to deal damage to opponents too.
Also, it seems the RNG only rolls when the menu is open, so the randomness is probably different from the first.
The same author also made a TAS of the first game in the (J) version:
http://www.nicovideo.jp/watch/sm6861809
Apparently, he didn't know the RNG manipulation techniques used in the published run and went with a different strategy. Instead of changing the deck before most duels, he made one with lots of cards like Bill, Prof. Oak, Recycle and Computer Search, which allow one to access more cards in the first turn.
That got him longer turns and made luck manipulation a lot harder though, he waited more frames and sometimes had to KO opponents with pluspowers or coin flips where it was possible to avoid it. He also couldn't manipulate Murray (it's a pain to get him with two Abras) and Mitch to be killed in two turns.
He also didn't use Defenders to stop the AI from attacking. Overall, despite the tutorial ending ~1:30 sooner in (J) version, his run is 4.2 seconds slower than the published (U) run.
Still, it's an amazing effort and his strategies could maybe be used to save time in a future revision.