They say a boat is a hole in the water that you pour money into.
A ship is just a larger hole into which more money must be poured.
While it would be great to see significant ships preserved (and I will let you define significant for yourself), the current economic situation just will not allow it. The Yorktown in Patriots Point, SC is falling apart due to lack of funds. (Hey Gov Sanford - how 'bout asking for a stimulus check!). The Hornet in SanFrancisco is in bad shape. The Texas is in need of a drydocking. The Stewart & Cavalla were ravaged by Hurricane Ike and haven't been made right. I fear that putting the Kennedy at Fall River or Quincy would draw from the volunteer staff needed to support their existing ships.
To support an aircraft carrier you need a large-enough tourist base that will pay their admission fee to keep the thing painted and turn on the lights. Boston, perhaps. New York has the Intrepid, they're full. Philly, no. The JFK is too big for Baltimore's Inner Harbor, . Norfolk/Newport News wouldn't be bad. They already have the Wisconsin, but ex-Navy might just support a carrier. Wilmington - nope. Charleston - nope. Savannah - nope. Perhaps Jacksonville/Mayport.
The funding to support a retired ship museum is an extensive and expensive proposition that needs to be thoroughly explored well in advance. It may be better to let it go than do a half-a**ed job.
My wet blanket opinions