1. Why is only Takae - Henoko - Futenma in the limelight when there is still a large number of other locations where bases affect both Okinawan residents as well as the environment on a daily basis?
A: Those three are the only locations where there's been noticable attempts by the U.S military to expand and strengthen their military operations in Okinawa.
In the case of Takae; 6 new helipads (one completed per date)
Henoko: Relocation plans of Futenma airbase to an offshore location just outside of Henoko town.
Futenma: In addition to it being situated in the middle of Ginowan city (one of the largest cities in Okinawa) and thus making it directly associated with any crime caused by U.S service personnel/plane crashes there, the recent deployment of Osprey aircrafts (notorious for their noise and high crash danger) has also made it an easy target for rallying together in resistance.
In other words, although the other bases also affect the public and the environment more often than not in a negative way, there's simply not enough new negative activity to enrage the public. For most people these days the sad reality is that they're just there and always have been.