Part of our problem last year was that when Moore went down injured, Hooper was a fairly obvious choice to become captain.
It says quite a lot about the other 14 starting players that a 22 year old who had played less than 30 tests was the next best option.
It should be a no brainer that a 32 year old Stephen Moore with 90 odd test caps should be a better choice for captain than Hooper.
The question of the vice captain is important as it is clear that Moore won't be on the field in the last 20 minutes of the match. Hooper could still be that person as even if we decide to play both Pocock and Hooper, their skillsets suggest that for better balance, Pocock is probably the starter.
In terms of Pocock, I think people conflate his excellent character off the field with his captaincy ability. As it stands we've seen very little evidence on the rugby field that he is a good captain.
One of the biggest things working in Hooper's favour is that so far he's been very robust and always been available for selection. It surely weighs on the mind of any coach when considering people for leadership positions who have a tendency to get injured often.
If all the likely parties are healthy, I'd bet on Moore as captain and Hooper as vice captain.