I know that. I never meant to suggest that they did everything in a few months. But they'd been working on hardware that wasn't the final stuff. Thus, when the final specifications and kits come out, you have to adapt everything you have to fit these and test everything. This can take a long time, certainly more than they've had with the final dev kits. That's where they ran out of time. It's one thing to have everything working beautifully on a PC that reproduces the new system fairly closely. But there's still much work to do to get it to work on the final hardware.
By your statement, you're saying that Madden was finished and this is how they wanted the final product to be. THere is no justification for this business wise. If they had wanted to save money then they would not have made the new engine. They would have simply ported everything over, features and all and that would have been cheaper for them than what they did.
Maybe you're right to a certain extent and the final kits don't explain everything. Maybe they just left themselves too little time for what they actually wanted to do. But at the very least, the game was unfinished. What we don't know is how much more would have been in there had they finished it. Many games have been delayed for the 360 so EA is certainly not the only one to have underestimated dev time. CH2K6, a straight port, was pushed back something like 4 months. That's probably what EA should have done with Madden.