People are over here talking about using Mei...

I still don't have her.

On a side note, I'd go for Shisui, he's just better in the current metagame, the pricing doesn't decide if they're good, it's their skills that do

Lets compare the two Nin, skill by skill

Mystery-Mystery

The only way Ao could win this is that it's cheaper, the condition lasts 3 rounds, and that it's on round 1, but most major mysteries don't come in until round 2, and there's immunity and healers that may remove the acupuncture prior to mystery usage. Whilst Shisui's is more expensive (by 20 chakra) and is activated round 2, it hits more people, inflicts a 2 round Chaos (better then Acupuncture), and removes shields and buffs to the person with Chaos, this CAN be healed, but it has a lot of damage. So...I kinda have to give this to Shisui, just better overall

Standard-Standard

Ao has the normal standard, whilst Shisui hits 2 people at once with Ignition, Shisui has more AoE and a status condition, and Ao's 3 combo really isn't too gamebreaking. Shisui has a better standard

Passives

Shisui has a dodge and a barrier, Ao has clones (which is good for stalling, and are good chakra batteries, but easily sweeped up by AoE attacks from Jinpachi or could give Kushimaru a free attack), and Shields. Ao is more of a generally defensive, earlier game ninja, while Shisui has more damage and the dodge, if he's in position one, will let him pull of his mystery on most occasions, the only exception would be if Minato (kage one) hit him with Raijin Kunai and ended up hitting him after his chase was activated. But Ao lacks one so...yeah. This is really up to preference, I guess, Ao is good early game, but Shisui has a tri-elemental barrier and a dodge, which are more viable late game and in modern game.

Chase-Chase

Probably the only place I'd give the win to Ao. Shisui would have to be paired with the 4th Raikage or Kage Minato for the Tag to be put to it's full use, and Ao has an acupuncture chase, which is always handy.

Personally, I'd suggest Shisui, since he's just overall a more solid ninja, and the fact that many others have pointed out he's easy to get in treasures.

Sure, a lot of people got Shisui for free, but there's a lot of people who didn't get him for free/not at all, I never got Shisui, he's just bait.