the thing is:
rikodou was the one that wrote on that "uchiha" stone. (so far, it is manga fact)
that stone has the secrets of mangekyou and the jubi thing. (so far, it is manga fact).
question: how rikodou knew about the mangekyou powers\secrets?
answer: rikodou was able to use mangekyou's powers, or better put, rikodou's rinnegan was able to use mangekyou's powers.
here goes the theory.
somehow madara and his brother discovered that by killing their best friends, they would achieve new powers.
only logical justification: they were the strongest uchiha and they trained and developed those eyes so much, that they were able to read more from that stone (young sasuke was able to read to the part that said that the new doujutsu was able to control kiuby). eventually, they read that by killing their best friends (or kill all the bonds etc), they would achieve MS.
this means that mangekyou's powers are really old and not a new thing. when sharingan is developed, it becomes "older" and closer to the "perfect rinnegan", or rinnegan level 2.
now you guys ask:
what the f*ck is rinnegan level 2 amazing and godly rinnebadass?
and i answer:
in the beginning of part 2, a pic from deva path was showed when they were going to seal ichibi. that pic clearly showed a 3 tomoed rinnegan. some you may think that it was a mistake (and perhaps it was, but not because kishi was confused between itachi and deva path, lol the eyes already have ripple patern) however i think it wasnt.
why? -it was something too big in a manga were the eyes are very important and are huge references.
- step 2
step 2: look at jubi's eye. what do you see? i see a rinnegan with nine tomoes (the perfect rinnegan. the one that was able to use mangekyou's powers too) and not jubi's ultimate sharingan. jubi is somehow in a "submissive" position. in my opinion, jubi is under the effect of rikodou's "tsukyomi" and rikodou's eyes are just like the eye that we can see in the ten-tails.
why nagato lost the tomoes:
the truth is that i have some doubts here. but i will do my best.
when nagato fought hanzou, he was able to jump, walk, and flex his legs even when he was hit. this is manga fact. however he stoped to move when he was pierced in every organ etc (you can understand why) by gedo mazo.
theory: after that fight, he trained and was developing those eyes. eventually his eye tomoes began to appear. after that, he started using gedo mazo several times 3 days in a row etc, and he was going weaker and weaker. still he had to fight for his village etc. he created pain and was becoming even more weaker etc. the tomoes disapeared.
another theories: perhaps tobi wants sasuke's ems to fuse them with the rinnegan.
tobi wants a strong sasuke and the rinnegan because he needs the rinnegan to summom gedo mazo and wants sasuke to be "sucked" by it.
this may be the moment when sasuke tries to stab tobi.
fact: even the rinnegan that we saw can counter any MS jutsu so far.