it looks like you just answered your own question......Because he wanted to retain his space time jutsus, although for himself not for his 6 paths.And i already mentioned this fact in an earlier post, so you did'nt bother to read it, that makes you the troll here.
he didn't take the second eye because he still wants his space time jutsus WHICH ARE ON HIS MANGEKYO and still get the benefits of RINNEGAN after doing the transplant
same happens with jinchurikis but with the benefits of sharingan(3 tomoe) instead of the benefits of MS....
now you feel me??