Hyuga/Kaguya are the descendants of Hamura, and Uchiha/Uzumaki are the descendants of Hagoromo, so why don't we pitch the prodigies of each side together? Left out Moon Otsutsuki and Senju for obvious reasons.
Neji: Prodigy and strongest of his clan.
Kimimaro: Prodigy and strongest of his clan. Also the only "survivor" of his clan.
Sasuke: Prodigy and strongest of his clan. Also the only survivor of his clan.
Karin: Prodigy maybe, but the "purest" of her clan.
Genjutsu is not allowed because Sasuke. Animal summonings are not allowed because Sasuke. In addition, Curse Mode is not allowed because I want them to use purely their original/clan's abilities. Susanoo and Adamantine Chains are not allowed though, because they're too OP.
This is during the war before Sasuke "died", so everyone has knowledge and abilities up to there, which means Sasuke can use EMS. Kimimaro is not an edo, so he can be killed, and he's not sick. The battlefield is an open grass field.
At first it might seem that Sasuke can just one shot all of them with Amaterasu, but Neji can release chakra from all tenketsu, which could possibly work just like Shinra Tensei. Kimimaro can also just cover himself with protruding bones so he can remove them if they got caught. Karin is here to heal and support Sasuke because he is versing 2 prodigies after all.
If it was base sharingan before mangekyo got involved then Neji and Kimmimaro stomp Sasuke hands down. Karin is pretty useless in a fight and neither of the enemy is going to let her heal Sasuke. With Mangekyo though Sasuke can take them both on cause its power is so cheap since he can look at people and set them on fire.
But would Genjutsu by sharingan work against an activated byakugan?(even though OP has clearly removed it from eqn regardless) I don't think Sasuke is gonna win without kirin or summoning. you have already covered about amaterasu. Susanoo(Armored) is probably equally matched with rotation and bone as defense, Though cost for keeping Susanoo up is much higher so my best guess Sasuke-Karin's team stamina runs out. (Any summoning would probably be killed by Kimimaro eventually.)
I don't really think, both of them could just react to Ameterasu....It's on eye point and only the Raikage has dodged it.
I don't think Tenkestu could work.But let's say it could do it like the Shinra Tensei.It doesn't actually mean it could work.Amterasu while burns slowly, it has shown to be powerful enough to neuterlize a bijju.The moment it's on the part of their body.It's not gonna be pleasent.Not at all pleasent.
MS Sasuke will win this fight.
But to the first comment that said "Three tomoe Sasuke will get beaten."
I would like to point out that Sasuke is still far stronger than the both of them.
Taking out CM,Genjutsu and Summoning.Sasuke has in his disposal,
2.A large Chakra supply and prodigy level chakra control.
5.A very remarkable speed.
6.Expert Taijutsu skills.
7.An Expert Tactical and strategistic mind with a calm attitude.
8.Chidori and it's variants.Especially Kirin.
9.And The Sharingan.Having the ability to see through every jutsu and find it's weakness.Like Neji's incomplete 360 degree vision, If the spider ninja guy(I don't remember his name) could could, then obviously Sharingan could find it.And as well as track fast moving objects.
Now this is my opinion.As Kimimaro died and Neji(Well what's the difference in him being alive in part 2?) has shown nothing impressive enough at part 2 to match part 2 Sasuke.
You guys may have a different opinion.But I'm gonna stay with mine.Peace.
The thing you should remember about Kimmimaro was he was dying of a disease and moving his body out of sheer will power. He was able to take on Gaara and Rock lee an opponent who bodied Sasuke when they first fought. A Kimmaro was going to be orichimaru's new host before he got sick. Kimmimaro is a monster who'd likely have styled all over sasuke if he only had base sharingan.