Hmm, I think that was more of just a design decision than anything. I'm not sure how well the game would work with joystick control, but then again I haven't played the iPad version. In any case, since the iPad version has been out a while, I doubt it's likely to change anytime soon, sorry. :/
It makes the game hard to play. My hand always ends up blocking the screen. Also i can never really relax while playing because i have to move my hand so far just to make the character go up a little bit. Overall it is not playable for me, so i deleted it. I will not be requesting a refund, because i love Aquaria and the $35 i have contributed to the brand($30 for the PC version and $5 for the iPad version) i am confident will go to future awesome games and making hopefully a sequel to Aquaria. In any case i just wanted to express my disappointment that the control scheme is keeping me from having a functional version of the game for iPad.