what pass best suits this trip?

Arrive at Haneda airport
Stay 4 nights in Shinjuku
Stay 2 nights in Hakone
Stay 4 nights in Kyoto
Stay 2 nights in Nara
Saty 1 night in Ise
Return to Tokyo night before departing

A Hakone Free Pass would make sense for you, of course, whether if it pays off depends on whether you use it enough to cover its cost:

http://www.japan-guide.com/e/e2358_008.html

If you remove one night from Kyoto, or just do Ise as a day trip, a 7 day JR pass will pay off from Odawara onwards (~33,000 yen, not including local segments, vs. ~29,100 yen for a 7 day pass). You would still have to pay around 510 yen from Kyoto to Ise, and again from there to Nagoya (because of JR trains using another company's tracks), assuming you use JR trains only.

If you do not want to do that, then from Odawara to Tokyo you have 8 days and cards for local trains and tickets for long-distance trains are likely better, and would enable you to take Kintetsu express trains to Ise, shortening the trip from Nara to Ise by an hour or so.