We are planning to visit Japan in April, and this our first visit to Japan. we are family of four (2 adults and 2 kids [9 and 6 years])

Our aim is to see Cherry blossom

Please advise your thought on our itinerary

11 April: Arrive at Narita 5:05pm. then we catch train from Narita to Kyoto

12 April: Kyoto we are plan to visit
- Philosopher's path for Cherry Blossom
- Kiyomizudera Temple
- Gion

13 April:- Fushimi Inari Shrine
catch a train from Kyoto to Osaka then do some shopping

14 April: Visit Osaka Universal Studio

15 April: Catch a train from Osaka to Hakone
We are planning to visit Resort spa (Hakone Kawakien Yunessun)

16 April: Catch a train from Hakone to Tokyo
before we catch the train we are thinking to visit lake Ashi to see Mt Fuji.

17 April: Tokyo Disney World

18 April: Tokyo Disney Sea

19 April:
- Ghibli studio
- Hello Kitty
- Puro land

20 April: do some shopping before flying home

During our visit in Japan we are planning to use 7 days JR pass, do you reckon this is enough? should we get Hakone pass if we have JR pass?

and last question what is the recommended hotel in Kyoto (convenience location [close to train station, shopping, supermarket and food :P])

Thank you in advance for your help

Overall it looks nice to me.

11 April: Arrive at Narita 5:05pm. then we catch train from Narita to Kyoto

Usually it is best if you take the Narita Express to Shinagawa Station and then transfer to an Hikari Shinkansen for Kyoto. Note that you won't arrive into Kyoto until quite late (probably 11pm). You may prefer to spend the first night in Tokyo.

12 April: Kyoto we are plan to visit
- Philosopher's path for Cherry Blossom
- Kiyomizudera Temple
- Gion

Seems fine. Maybe pick some other spots from here also:-
http://www.japan-guide.com/e/e3951.html

13 April:- Fushimi Inari Shrine
catch a train from Kyoto to Osaka then do some shopping

Osaka Shopping Guide
http://www.japan-guide.com/e/e4013.html

14 April: Visit Osaka Universal Studio

This is a Sunday and likely to be busy.

15 April: Catch a train from Osaka to Hakone
We are planning to visit Resort spa (Hakone Kawakien Yunessun)

Seems fine.
Hakone access
http://www.japan-guide.com/e/e5206.html?aFROM=2157_5200

16 April: Catch a train from Hakone to Tokyo
before we catch the train we are thinking to visit lake Ashi to see Mt Fuji.

I'd probably do the Hakone Round Course with the Hakone Free Pass
http://www.japan-guide.com/e/e5210.html

17 April: Tokyo Disney World
18 April: Tokyo Disney Sea

Ok.

19 April:
- Ghibli studio

Note ticket purchasing details as they must be pre-purchased.
http://www.japan-guide.com/e/e3041.html#jump_hours

During our visit in Japan we are planning to use 7 days JR pass

Sounds fine.

should we get Hakone pass if we have JR pass?

Yes if you wish to do the round course.

and last question what is the recommended hotel in Kyoto (convenience location [close to train station, shopping, supermarket and food :P])

You don't mention price. It is peak time in Kyoto so some of them may have minimum night restrictions and they may not be cheap.

Two common options are Granvia Kyoto and Hotel Hokke Club Kyoto.

Book soon if you can.

If you can't find anything in your budget for those dates (you stay a Friday night) then you can consider staying in Osaka and visiting Kyoto as an easy day trip. If you stay near JR Osaka Station then the trains are covered by the JR Pass and take around 30 minutes each way.

11 Apr: Arr at Narita 5pm

12 Apr: we going to visit
- Shinjuku Gyoen (Cherry blossom)
- Chidori Gafuchi (Cherry blossom)
- Puroland (optional)
- Ghibli Museum
- Harajuku

13 Apr: catch train from Tokyo to Kyoto
- Philosopher's Path (Cherry blossom)
- Kiyomizudera (Cherry blossom)
- Gion

14 Apr:
- Fushimi Inari Shrine in the morning
Catch train from Kyoto to Osaka
- Denden Town
- Shinsaibashi

15 Apr:
- Universal Studio

16 Apr:
- Osaka Aquarium
Catch train from Osaka to Hakone
- Hakone Kowakien Yunessun

17 Apr: Hakone Round Course with the Hakone Free Pass
- Hakone Tozan Railway
- Owakudani Valley
- Lake Ashi
Catch train from Hakone to Tokyo

18 Apr:
- Disney World

19 Apr:
- Disney Sea

20 Apr:
- Tokyo Tower
Evening fly home

Since our 7 days JR pass expired on the 17 Apr, Based on your experience is it better for for us to get 14 days JR pas for the rest 3 days in Tokyo or is there a better alternative.

Thank you so much for your help

Definitely do not get the 14 day JR Pass.

Letting the 7-day JR Pass expire on the 17th is fine.

It depends a little on where your hotel is located but it might be slightly better to buy the Suica + NEX return package at Narita Airport. Use the NEX to get you into Tokyo on Day 1 (and back on the last day), use the Suica to get around Tokyo while you don't have a JR Pass.
http://www.japan-guide.com/e/e2359_suica_nex.html

Then you can set the activation date of the JR Pass as April 12 (or April 13). Note you should still do the exchange of your exchange order for the actual JR Pass at Narita, just specify the date (12 or 13) when you do so.

That way your return from Odawara (Hakone) to Tokyo is covered on the 17th.

Even if you don't do any of the above individual tickets for your last few days without a JR Pass are likely to be the best/cheapest option.

If you purchase the air ticket that allows you to return from a different arrival point, it's easier than back tracking.