How many people man the site? What are their qualifications? How can we be sure there is no personal prejudice? How many camera feeds do they have? Do they have to provide a written explanation of their calls? Who pays them? Is Jake still in charge?
I have lately thought that instead of the command centre overturning or upholding a call on challenge, they should just clarify the rule and replay the challenged play in slo-mo and from different angles for the benefit of the head official and the official who actually made the call. After seeing the play at different speeds and from different angles, and getting the league competition committee interpretation, the two officials on the field can reverse the call or uphold it. Then we all live with the result, whether we feel it was a "good" or "bad" one. Usually TSN takes a commerical break during the review process anyway, so it wouldn't really add much time or interrupt the flow. Coaches initate the challenge anyway.
The command centre could still review scoring plays and turn-overs, although what the heck they review I don't know. If the command centre wants to change something, I feel it still goes through the head official who has the authority to veto.
I also like the suggestion made elsewhere, that the guys who go fishing should get a yardage penalty if the call is upheld. Put the game back into the hands of the on field personnel.