It sounds like you are visiting Hakone.staying at prince hotel, going for the lake cruise and cable car only, as well the local transport to/from this two place.is that worth to have the pass for 2 destination plus local transport?
Yes, but note that access to the Prince Hotel is not straightforward with the Hakone Free Pass. Quite a few of the buses to the hotel are not covered. I think the best way of access, using the pass would be by Odakyu bus from Togendai.
Also note that the cable car between Gora and Togendai ("Hakone Ropeway") is fully covered by the Hakone Free Pass, but the cable car up Mount Komagatake (nearby the hotel) is not fully covered.
Likewise, note that the pirate ship shaped sightseeing "Hakone Sightseeing Boats" that operate between Hakone-machi, Moto-Hakone and Togendai, are covered by the pass, but that the "regular looking" sightseeing boats that also stop near the hotel, are not.
So, if you intend to take the Komagatake Cable Car and the cruise to the pier near your hotel, the Hakone Free Pass will not be valid.
In that case, it might be better to use the "Hakone Smile Coupon", which is valid on all the Prince Hotel related buses, ships and ropeways:
http://www.izuhakone.co.jp/smile/index.htm