I guess it all depends on the final product you're after. I upgraded from a NEX-7 to a6500 Nauticam housings and enjoy the better AF and IBIS (miss Tri-Nav though). I shoot super-macro most of the time and MF is the most common focusing method, so focusing systems come more into play more in video and fast action shots. The a6500's IBIS helps with lens that don't have built in stabilization. I've set up my rig to shot with the very sharp and bright Sigma 16mm f1.4 in a 4.33 dome. f1.4 is a nice fast lens for underwater video and has fairly fast and accurate focusing. Use this with Sony's "Clear Image Zoom" function and a 15X diopter and you have some incredible footage in macro or WA using one lens (and swing diopter). For those scratching their heads and thinking Sigma 16mm f1.4 in compact 4.33 dome with diopter? I got the lens to fit by filing off the shade support mechanism and grafted a swing diopter mount from my old Flat Port 72 onto it's wings (not for the faint hearted..it was a lot of work), but I love that stuff.
Still photography fast action shooting will always benefit from improving focus systems like the a6400 and new a6600 have. I'm happy with my upgrade from the NEX-7 to a6500 though with the latter being no slouch in the arena of AF. Perhaps not as accurate as the new system in the 6400/6600 but I wonder how much? Worth the extra buck when you can pick up clean used a6500 housings and camera now that the latest and greatest a6600 are out (just a matter of time for Nauticam, they never miss a beat.....
Using some creative modifications, I now shoot Sony 18-55 (single dive Macro & WA set-upset-up), Sony/Ziess 16-70, Ziess Touit 12 and Sigma 16mm f1.4, all in my compact 4.33 dome (w/ swing diopter CMC-1 for macro with appropriate lens) using a mix of 20-50mm of mini-extensions. Great travel rig. However, I also added the Sony 90mm macro housed in the N100 manual focus port system which added to it heft, but nice sharp and long macro lens in APS-C format.
Have fun with your new rig whatever you get :-)