When 004 eventually hits the water it will be interesting to see how many of the 'faults' and 'deficiencies' in the 003 design picked up by SDF members are actually resolved
There are many improvements that 003 could undergo in a successor design, but new design would also require a larger ship to enable some of those improvements to be undertaken in the first place. Not to mention the improvements that would be facilitated by the prospect of nuclear propulsion.
In the case of the placement of the catapults, as it has already been mentioned, the operation of the catapults and elevators simultaneously should not be an issue as the flight deck should operate in a cyclical manner anyhow.
There would of course be some benefit in having greater clearance between the two, but that would also require a longer ship to enable moving the catapult and the catapult launch position forward by about 10 meters or so.