It doesn't have to have such a tremendously detailed reason for being changed. Really, it's very simple.
The changes being:
Brighter blue
Yellow S on the cape.
A redesign of the waist area to make room for a thin red belt of some sort.
Clark and Lois can clear this up in a short and simply conversation, which could be done right at the beginning of the movie after a tremendously fantastic opening sequence.
On their way to the Planet, after Supes has quickly changed back to Clark and is discussing what just happened with Lois and which one of them will get the "Scoop" on this one.
Lois: Good job. People are warming up to you.
(smiling) Love the changes the changes to the suit by the way, looks less....alien!
Superman: (Contently) Exactly.
That simply line "People are warming up to you" Explain so much of what took place in MOS, and how some people might still be blaming Superman for what they know or may not know was an inevitable confrontation between Supes and Zod.
It's not to imply in any way that he's distancing himself from his heritage, but just that he's a citizen of Earth now and wants people to see him for what he's trying to do. Because let's face it. The current suit, ( And I really must stress that I DO like it, a lot) It's so dark and metallic looking and that's generally not very terrestrial in appearance and I wouldn't put it past Clark being concerned that the second people see him they will immediately think " ALIEN", which he obviously is, but Earth is and always has been his home as far as he's concerned and his appearance needs to reflect that. It's not any more complicated than that.