Yeah, I can see your worry Azure. Although, I think it's a smart strategy on SE's part given how the quality of Chrono Trigger compares to the quality of the average iPhone RPG. Visuals are about on par, and its story still blows most iPhone RPG stories out of the water -- we can thank obscenely poor quality translations for that, and maybe a "story doesn't really matter, just chuck any old thing in there" attitude among game developers nowadays. If SE wants to pump some money into it and take advantage of the iPhone 4's Retina Display, maybe we'll even get HD sprites out of this. Hah, I love wild speculation!
BTW, Secret of Mana is coming out on the iPhone soon, so SE has already proven its like of SNES-to-iPhone ports. In any case, the prediction is that we'll know by the end of this year, so we can make a call on December 31 I guess.