Your OP have a lot of merit, I'll just disagree on the Sony Corp interference or demanding the shift in tone.
It was probably decision by the studio itself, unless you have some source or evidence for this because from all we know Sony allowed a lot of freedom for devs.
The shift for more mature themes and more violence in ND games have been growing ever since.
Whatever the case was, It always felt unnecessary IMO. Like this wasn't made darker because they had new ideas to explore with a darker tone, it felt like was made that way because a focus group of edgy 12 year olds thought colorful platformers were an outdated and kiddy concept, and GTA3 was the new hotness. It just signaled to me that ND wasn't very confident in their own creativity.