In Naples is it probably less likely that Louis will clash with his brother. So he will stay King, which could actually help Napoleon, because Louis was a better soldier then Jerome and more loyal in the end as Murat.
If Louis goes to Naples I assume Josef goes to Holland. This means, if he still goes to Spain, Murat will become king of Holland. With Murat King, Holland will probably not get annexed and its possible the German coast will go to Holland.
This means major butterflies for the events in 1812/13.