I'm not sure why you think that performance on an ipad 3 in retina mode is that bad. On my sprite test, someone with an ipad 2 said they got about 450 sprites at 60 fps, from 350 on an ipad 3. That's a noticeable difference, but far from bad performance in comparison. My ipad 3 is easily powerful enough for the Zelda-like game I'm making, playing at a smooth 60 fps with dozens of enemies onscreen, and the only reason the fps dips below 60 if I add more is because of the JavaScript, not the rendering, because if I disable the game logic I can have tons more onscreen at 60 fps.
Might it have to do with the fact that performance when previewing over LAN is somewhere around a third or less of the exported HTML's performance? I only get about 100 sprites in my sprite test when previewing over LAN.
Regardless, I think I may have actually found a way to fix this, but I need to make sure it works on multiple devices. I started a thread with the test here: edit, test was flawed, had issues making it difficult to get an accurate result