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In this alternate universe the Uchiha clan never planned a rebellion and are still a part of Konoha. On a mission Nagato killed Sasuke(13 years old) and left Itachi wounded. Seeing his little brother die awakened the power of Mangekyou within Itachi. Using DNA from Sasuke, Nagato revives the original Madara Uchiha(somehow...don't argue about it). Two years later; after having mastered Mangekyou Itachi finds out that his brother's death was planned by Tobi in order to bring back Madara. The furious Uchiha vows to avenge his brother.
Madara can use Amaterasu and Tsukuyomi in all scenarios. If either is caught by Tsukuyomi they can survive it but suffer losing chakra. Itachi loses 1/3 of his chakra and Madara loses 2/3. Itachi can use all powers he has shown.
Scenario 1: Itachi(no illness, has sacred weapons) meets Madara at the Uchiha hideout. Madara is sitting on the thrown and Itachi enters with killing intent. He has a little more Chakra than Kakashi. He can't use a full powered Susano'o as long as Sasuke. Madara has EMS but doesn't have the kyuubi and also has killing intent. Madara has as much Chakra as current Sasuke.
Scenario 2: Itachi(no illness, has sacred weapons and Sasuke's Mangekyou) meets Madara at the valley of the end(or whatever the hell it's called) They meet up on the water. Itachi can use Sasuke's EMS abilities. They both have killing intent. Madara has EMS and the Kyuubi. Itachi has Sasuke's chakra added on to his own.
Scenario 3: Same as scenario 2 except Madara also has Tobi's space/time jutsu.
Scenario 4: Itachi(no illness/w sacred weapons, Sasuke's mangekyou and Kyuubi) meets Madara(no space/time jutsu but has rinnegan and senju powers) at an abandoned Uchiha town in Konoha. There is a Super Duper Force Field around the town stopping anyone from entering or leaving. Itachi has Sasuke's abilities and chakra. Madara's chakra is tripled.
Itachi win in every Scenario with Sword of Totsuka and Yata Mirror. Easy win.
Itachi winning (lol²) easy (lol³) against EMS Madara with Kyuubi and Space/Time Jutsu?
How will a fight between Rikudou Sennin with full Jyuubi control and Itachi end? Of course Itachi would win, I think we all agree with this. The question should be if Rikudou Sennin would able to make a second scratch on Itachis forehead protector or not?
Edit: I will post my opinion about the scenarios later.
full powered Susanoo for ~1-3 seconds against Kakashi.
Scenario 1, Susano'o with the Sword of Totsuka wins against Susano'o without it.
Scenario 2, despite having a weaker Susano'o, Susano'o with Kyuubi wins.
Scenario 3, same, only easier
Scenario 4, the Susano'o with Rin'negan and Hashirama's powers wins thanks to flower world after/before suppressing the Kyuubi.
I agree completely with Uchiha_Blood. Itachi wins the first scenario, Madara sweeps the other three.