Instead of reducing Kassadin E cooldown how about reducing the Charge needed with level.

What if his ult gave him 2 charges on it?

The further you go into the game the less you have to think about your mana. (apart from ult stacks). So decresing stacks over leveling it up won't be too useful. Especially since teamfights charge it back up to 6 stacks in a few seconds. So getting a lower cooldown will allow you to use it more.