Both games were built on the same foundation. The games were just tuned differently so they would play differently, mainly NCAA being more wide open. Both games would get things added that the other wouldn't get for a year. Madden typically got the bigger additions first, like the physics.
Both games had their natural differences, too, like the obvious rule differences between the two games, recruiting being a part of NCAA.
I would expect the reboot to be exactly like this. We've already see with PC modding that Madden is able to be tuned to play much differently when made to play more like the college game.
Hopefully EA can nail the feel down and deliver us a good game. I do wish it were coming to PC and would be able to be modded, but that doesn't look like it will happen, unfortunately.
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