Imo, in terms of skillset, MS Sasuke had superior amaterasu control(Enton) while MS Itachi had superior genjutsu control(Tsukuyomi) from their respective comparison done by C and Danzo respectively, and in terms of Susanoo, MS Sasuke only reached the max power of his Susanoo against Kakashi, but he didn't even have time to use it for long considering he lost eye-sight due to overusing his MS in continuous battles in a short timespan, when Itachi at one point managed to reach the max power of his MS in the long years he had in his MS usage, so in terms of skillset, overall MS Itachi overall had superior skillset to MS Sasuke until the short moment he managed to complete his Susanoo against Kakashi, where they ended up about equal in terms of skillset, but for a short amount of time.
Skillset aside though, Sasuke implied that Susanoo destroyed his cells when he was just using partial version of it during the Kage summit, wondering how it was for Itachi who had the complete version, with Itachi's health also deterioriating all the more the moment he was using Susanoo, noticed by Zetsu, all of which suggesting then, that it's something Itachi couldn't use for long, maybe due to his lower chakra reserves, with the costs of MS implied to still be an issue for him even in part1(was visibly exhausted after using 2tsukuyomi, 1 amaterasu to the point of deactivating his sharingan).
And seeing how trigger happy MS Sasuke was, with his arrows being very hard to dodge, in a 1 on 1, Danzo fight MS Sasuke may have managed to push Itachi to overuse Susanoo and outlast him in MS usage, with his genjutsu forte(tsukuyomi) not working, while on the other hand, amaterasu playing more in Sasuke's favor due to his superior enton control, but while at the same time, only matching the full level of Itachi's Susanoo against Kakashi.
On the other hand, early EMS allowed Sasuke to use the complete form of his Susanoo more often, solved the MS drain problem while Itachi got his own version of "EMS" due to his edo version not feeling the body drain side effects and having his chakra replenished after a certain amount of time.
And afterwards, EMS Sasuke continued his evolution from the Jubito battle and up