Tokyo-Kyoto-Disneyland

Hi,

I'm planning a 11 days trip in May with 2 adults and one child (3y/o but thinking of getting him a ticket as well).
Here's what I have in mind, we'll be based near Shibuya.
Day 1- N'EX to Shinjuku
Day 2/3- Explore Tokyo
Day 4- Day trip to Nikko
Day 5- More time in Tokyo
Day 6- Day trip to Hakone
Day 7- Tokyo to Kyoto
Day 9- Kyoto to Tokyo Disneyland

Is it worthwhile to have the 2 weeks pass or should I pay for the N'EX and use the 7 day pass for later part of the trip?

Many thanks.