Timothy Chang said:
McMillen also believes that the remake will be done by a publisher who will rebuild the game using a different engine other than Flash, as McMillen has run into several problems with Shockwave with a game of Isaac's scope. "The flash version cant be updated anymore," he explains. "The file size is so large that it takes 10-15 trys to export a functional swf file.. if we add or edit anything it gets worse and worse and is getting to the point where the fla becomes corrupted every other save.. we cant add anything without breaking EVERYTHING."
Yeah, i noticed when since Wrath of the lamb there was one game breaking bug after another. Him complaining "But I want to be done with isaac T_T" after every fix didnt help either.
Some of the worst bugs are out, but tons are still left:
http://bindingofisaac.wikia.com/wiki/The_Binding_of_Isaac:_Wrath_of_the_Lamb/Bugs
He should have thought earlier about the flash limitations and as much as i like the game, i wouldnt buy the whole thing again after that.