Hi I'm a HUGE DC fan and me and my sister have been watching this since DC first came out and I just wanted to share my opinions! ^.^~!!
I believe that Mitsuhiko might be Anokata and that Professor Agasa might be the "highest ranking member' of the Black Organization.
Heres why:
1.) Mitsuhiko - high possibly of being the boss. although theres many holes as to how he became a kid and for what reason he took the pill to become small, because the pill was orginally meant to kill right? I was thinking a minor character that died in the hands of the BO made the Anokata take the pill on accident? such as Ai-chan's sister?
2.) As mentioned in many previous posts, Agasa is highly speculated to be Anokata. I believe he's a major member of the BO and the only reason he's housing Ai-chan is to find a solution (or rather, pill) to countereffect the APTX 4869 (shrinking pill) for Mitsuhiko.
Gosho mentioned that we would be surprised- as well as Haibara right?
That means for Agasa to be the Anokata would be too expected, therefore the possibility of him being the boss might be small- although possible.
also, I read that Gosho mentioned that even Ai-chan is comfortable around the boss, meaning her BO radar off.
therefore wouldn't Mitsuhiko be a highly possible suspect as Anokata?