Mike, with my limited experience (3 nights in each place with only just days of diving) I believe that:
1) Rangiroa has more diverse marine life: dolphins, mantas, all kinds of sharks (silver, black white tips, grey and great hammerheads) and plenty of fishes the drift dives are exhilarating! In Fakarava Sud, the pass in narrow hence you see the sharks in a very concentrated formation really beautiful
2) Fakarava has pristine corals, they are almost 100% intact, it is really beautiful
3) Rangiroa has better topside options - im IMHO - if that matters for you. Hotels and pensions are better (warm water) and restaurants as well, Fakarara is very raw (I did not have cell phone, at Tetamany Village not even scuba instructors have internet access) but some people think this is a plus
4) The boat to Fakarava Sud can be pretty rough if you get winds and tides
5) Both places are amazing and you are going to love either way
6) Looking back I would have stayed the whole period in Rangiroa (because of non diving wife) and would have planned a whole weekend at Fakarava to dive also the north pass
7) If you go to Rangiroa do the sunset dive, it is very beautiful seeing the matting activity of surgeonfishes. If you go to Fakarava do a night dive, it is amazing the amount of sharks you will be surrounded by
Regarding liveaboards, I recommend looking into Aquapolynesie (
Acueil) since a couple I met in Rangiroa stayed with them in Fakarava and apparently liked a lot!
You are going to be spoiled, very spoiled after this dive trip
Here is my trip report (in case you did not see it):
http://www.scubaboard.com/forums/the-pacific-islands/514025-french-polynesia-trip-report.html