Actually Yu-Gi-Oh! GX wasn't in that situation. The GX manga was created while season 1 was airing.
CN didn't ask them to make more episodes, but it wouldn't be the first time an American company has. Duel Masters 1.5 was an American only season. The last season of Ultimate Muscle was created because 4KiRAB asked for more episodes and agreed to help fund it. DICE, Transformers Armada, Transformers Energon, Transformers Cybertron, and SD Gundam were anime series created by American companies (BANDAI Entertainment instead of Sunrise and Hasbro) instead of their Japanese counterparts. Sonic X season 3 was created because of the foreign ratings, much like Bakugan is (though it's based more off the to profits instead of ratings this time), but it too was done by the original companies, just as Bakugan is. As far as the beginning goes, the song for the dubbed version is the same, and the ending is basically the same with updated credits.
Actually no, a second series wasn't being made, though they did have possible plans. It was announced only 6 months ago. CN had a huge role to do in it. Bakugan has borabed ratings wise, but the toys have sold like crazy, and since CN gets profit from the toys, they wanted more episodes so they could continue to gain profit that way. As a result the worldwide premiere of Bakugan Battle Brawlers: New Vestroia isn't in Japan. Instead it is on Teletoon in Canada, since Nelvana is once again dubbing it and Corus owns both Nelvana and Teletoon.