If what Bikas says is true, then even Kohli, Dhawan, Rohit should have been rested for the whole series. After having sent them till Zimbabwe who would not like to have a series win under his belt. This is exactly what Kohli has done. He would definitely like to pitch in for the captaincy next when Dohni moves out.
Secondly Mishra is a leg spinner and is the only living Indian wrist spinner and cannot be compared to Ashwin who might have a better record. He may have crossed 30 but is bowling so beautifully and should be an automatic choice against South Africa.
Rest and the Sundry we can definitely leave out Vinay Kumar but not Unadkat who is an aspiring young fast bowler who has been given some chances to prove himself.
Overall if this were a mistake, not by Kohli but by the selectors.
kohli is not yet a matured captain...his very first intention was to win series so that to prove himself as successful captain. testing of bench strength come later and possibly can be seen in next few matches.